Contacts of the helix formed by residues 1069 - 1091 (chain G) in PDB entry 2VKZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO1069 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809G LYS* 3.9 26.7 - - + -
810G GLU* 3.2 10.8 - - - +
1067G ASP 3.5 8.3 - - - +
1068G GLU* 1.3 88.2 - - + +
1070G ILE* 1.3 60.9 + - - +
1071G LYS* 4.5 5.6 - - + +
1072G SER* 2.8 36.6 + - - +
1073G ILE* 3.3 4.0 + - - +
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Residues in contact with ILE1070 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594G VAL* 4.6 0.9 - - + -
606G PHE* 3.7 9.9 - - + -
609G ALA 4.4 4.0 - - - +
610G THR* 3.6 37.9 - - + +
613G ALA* 4.4 2.2 - - + -
805G VAL* 3.6 30.7 - - + -
808G ALA* 3.8 8.7 - - + +
810G GLU* 2.4 38.4 + - + +
1068G GLU 3.4 2.2 + - - -
1069G PRO* 1.3 69.9 - - - +
1071G LYS* 1.3 67.6 + - + +
1073G ILE* 3.1 15.4 + - + -
1074G MET* 3.1 41.3 + - + +
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Residues in contact with LYS1071 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576G LYS* 6.1 1.2 - - - +
612G ASN 5.6 0.6 + - - -
613G ALA* 3.5 46.3 + - + +
615G TYR* 4.8 0.2 - - - -
810G GLU* 3.9 1.3 + - - +
1069G PRO* 3.1 6.2 - - + -
1070G ILE* 1.3 80.2 - - + +
1072G SER* 1.3 57.7 + - - +
1074G MET* 4.3 2.3 - - - +
1075G ASP* 3.0 58.0 + - - +
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Residues in contact with SER1072 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068G GLU* 3.1 21.6 + - - +
1069G PRO* 2.8 25.3 + - - +
1071G LYS* 1.3 79.5 - - - +
1073G ILE* 1.3 53.2 + - - -
1075G ASP* 3.9 3.3 - - - +
1076G GLY* 2.6 33.8 + - - -
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Residues in contact with ILE1073 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772G GLY 5.0 0.4 - - - +
804G ARG* 3.3 57.2 - - + +
805G VAL* 4.5 4.0 - - + -
807G ILE* 5.9 1.3 - - + -
808G ALA* 4.2 18.8 - - + +
1065G VAL 5.7 0.7 - - - +
1068G GLU* 3.4 35.7 - - + +
1069G PRO 3.7 9.6 - - - +
1070G ILE* 3.1 8.2 + - + +
1072G SER* 1.3 75.9 - - - +
1074G MET* 1.3 81.5 + - + +
1076G GLY* 3.4 1.4 + - - -
1077G ILE* 3.2 26.1 + - + +
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Residues in contact with MET1074 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592G LEU* 3.9 8.7 - - - +
593G LEU 5.2 2.7 - - - -
594G VAL* 4.5 12.8 - - + -
613G ALA* 6.1 0.2 - - + -
615G TYR* 3.3 54.7 + - + -
801G PHE* 4.4 18.6 - - + -
805G VAL* 3.8 22.4 - - + -
1070G ILE* 3.1 29.0 + - + +
1071G LYS* 4.3 1.1 - - - +
1073G ILE* 1.3 97.1 - - + +
1075G ASP* 1.3 65.5 + - - +
1077G ILE* 3.0 26.8 + - + +
1078G HIS 3.0 10.6 + - - -
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Residues in contact with ASP1075 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576G LYS* 5.4 6.6 + - - -
613G ALA 4.8 0.2 - - - +
615G TYR* 2.8 25.1 + - - -
1071G LYS* 3.0 57.5 + - - +
1072G SER* 3.9 3.4 - - - +
1074G MET* 1.3 75.5 - - - +
1076G GLY* 1.3 57.3 + - - +
1078G HIS* 3.2 2.1 + - - +
1079G ASP* 2.7 52.9 + - - +
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Residues in contact with GLY1076 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774G ALA* 3.9 4.6 - - - +
1072G SER 2.6 24.0 + - - -
1073G ILE* 3.7 2.2 - - - -
1074G MET 3.2 0.2 - - - -
1075G ASP* 1.3 72.6 - - - +
1077G ILE* 1.3 60.9 + - - +
1079G ASP* 4.3 3.7 - - - +
1080G GLY* 3.2 18.9 + - - -
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Residues in contact with ILE1077 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592G LEU* 3.5 29.8 - - + -
772G GLY 4.1 11.7 - - - +
773G SER* 3.7 3.6 - - - -
774G ALA* 3.0 47.9 - - - +
801G PHE* 3.5 42.2 - - + -
804G ARG* 5.2 0.4 - - + -
1073G ILE* 3.2 17.5 + - + +
1074G MET* 3.0 17.7 + - + +
1076G GLY* 1.3 74.8 - - - +
1078G HIS* 1.3 68.0 + - - +
1081G HIS* 3.0 18.0 + - + +
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Residues in contact with HIS1078 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576G LYS* 5.3 5.8 - - - -
577G ILE 3.5 24.2 + - - -
578G PHE* 3.8 10.5 - + - -
579G VAL* 3.0 47.1 + - + +
590G PRO* 3.3 36.8 - - + +
591G PRO* 4.6 3.1 - - + -
592G LEU* 3.9 11.7 - - + -
615G TYR* 3.5 19.8 + - - +
1074G MET 3.0 6.3 + - - -
1075G ASP* 4.0 2.2 + - - +
1077G ILE* 1.3 76.6 - - - +
1079G ASP* 1.3 67.5 + - - +
1081G HIS* 3.1 4.8 + - + +
1082G ILE* 3.0 26.6 + - + +
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Residues in contact with ASP1079 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075G ASP* 2.7 41.5 + - - +
1076G GLY* 4.3 3.8 - - - +
1078G HIS* 1.3 77.7 + - - +
1080G GLY* 1.3 59.3 + - - +
1082G ILE* 3.0 35.9 + - + +
1083G LYS* 3.2 18.9 + - - +
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Residues in contact with GLY1080 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774G ALA* 4.0 10.8 - - - -
1076G GLY 3.2 15.2 + - - -
1077G ILE 3.7 2.9 - - - -
1079G ASP* 1.3 77.5 - - - +
1081G HIS* 1.3 62.1 + - - +
1083G LYS* 3.6 9.6 + - - +
1084G LYS* 3.1 33.2 + - - +
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Residues in contact with HIS1081 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579G VAL* 4.1 14.8 - - + +
592G LEU* 5.0 4.2 - - + +
774G ALA* 3.0 33.8 + - + -
777G THR* 2.4 40.1 - - + +
778G TYR* 3.9 18.2 + + - -
781G LEU* 3.1 32.0 - - + +
799G PHE* 4.0 13.7 - + - -
1077G ILE* 3.0 17.4 + - + +
1078G HIS* 3.4 11.4 - + - +
1080G GLY* 1.3 76.3 - - - +
1082G ILE* 1.3 59.1 + - - +
1084G LYS* 3.7 1.7 + - - +
1085G LEU* 3.1 32.4 + - - +
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Residues in contact with ILE1082 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569G LEU* 3.4 29.1 - - + +
577G ILE* 3.5 50.3 - - + +
578G PHE 4.3 0.4 - - - +
579G VAL* 4.3 3.4 - - + -
1078G HIS* 3.0 28.0 + - + +
1079G ASP* 3.0 28.0 + - + +
1081G HIS* 1.3 78.1 - - - +
1083G LYS* 1.3 63.8 + - + +
1085G LEU* 3.5 1.7 + - - +
1086G LEU* 2.9 30.8 + - + +
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Residues in contact with LYS1083 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079G ASP* 3.2 23.5 + - - +
1080G GLY* 4.0 8.3 - - - +
1081G HIS 3.3 0.4 - - - -
1082G ILE* 1.3 79.9 - - + +
1084G LYS* 1.3 61.9 + - + +
1085G LEU 3.1 1.3 - - - -
1086G LEU* 3.0 9.5 + - - +
1087G HIS* 2.9 30.9 + - - +
1092G ASP* 5.0 0.5 - - - +
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Residues in contact with LYS1084 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774G ALA* 5.2 2.0 - - - +
775G ASP* 2.9 44.6 + - - +
778G TYR* 3.4 53.6 + - + +
1080G GLY* 3.1 20.6 + - - +
1083G LYS* 1.3 76.6 - - + +
1085G LEU* 1.3 56.3 + - - +
1087G HIS* 3.8 5.3 - - - +
1088G GLN* 3.1 28.2 + - - +
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Residues in contact with LEU1085 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567G PRO* 4.0 24.9 - - + +
568G LYS* 3.8 16.6 - - - +
569G LEU* 3.9 17.9 - - + -
579G VAL* 3.7 30.3 - - + -
778G TYR* 3.3 24.2 - - + +
781G LEU* 4.6 4.0 - - + -
782G THR* 5.6 0.2 - - - +
1081G HIS 3.1 19.2 + - - +
1082G ILE 3.7 4.3 - - - +
1084G LYS* 1.3 76.0 - - - +
1086G LEU* 1.3 66.3 + - - +
1089G TYR* 3.1 43.5 + - + -
1090G TYR* 3.4 10.7 - - + -
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Residues in contact with LEU1086 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569G LEU* 3.8 11.2 - - + +
577G ILE* 6.2 0.9 - - + -
1082G ILE* 2.9 20.9 + - + +
1083G LYS* 3.3 9.2 - - - +
1085G LEU* 1.3 75.5 - - - +
1087G HIS* 1.3 58.3 + - - +
1090G TYR* 2.8 58.8 + - + +
1091G GLY 3.2 3.3 + - - -
1092G ASP* 3.3 30.2 + - + +
1093G ASP 3.9 15.5 - - - +
1094G GLU* 3.8 21.3 - - + +
1097G ILE* 4.2 12.3 - - + -
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Residues in contact with HIS1087 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083G LYS 2.9 14.8 + - - +
1084G LYS* 3.8 7.2 - - - +
1086G LEU* 1.3 79.1 - - - +
1088G GLN* 1.3 75.3 + - + +
1091G GLY* 3.6 12.6 + - - -
1092G ASP* 3.3 37.2 + - - +
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Residues in contact with GLN1088 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778G TYR* 3.5 27.1 + - + -
782G THR* 4.5 6.9 + - - +
784G GLU* 5.6 3.0 + - - -
1084G LYS 3.1 15.3 + - - +
1087G HIS* 1.3 91.4 - - + +
1089G TYR* 1.3 104.6 + - + +
1090G TYR 3.9 0.3 + - - -
1091G GLY 4.8 0.7 + - - -
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Residues in contact with TYR1089 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562G LEU* 5.3 4.0 - - - +
566G HIS* 3.3 40.9 - + + +
567G PRO* 5.2 2.7 - - + -
778G TYR* 4.1 1.6 - - - -
782G THR* 3.7 23.1 + - - +
1085G LEU* 3.1 38.2 + - + +
1088G GLN* 1.3 109.0 + - + +
1090G TYR* 1.3 79.1 + + + +
1091G GLY 3.8 0.7 - - - -
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Residues in contact with TYR1090 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567G PRO 5.8 0.2 - - - -
568G LYS* 3.9 13.2 - - - +
569G LEU* 2.9 57.5 + - + -
1085G LEU* 3.4 12.6 - - + -
1086G LEU* 2.8 31.9 + - + +
1089G TYR* 1.3 88.1 - + + +
1091G GLY* 1.3 67.1 + - - +
1092G ASP 3.2 1.0 + - - -
1093G ASP 3.2 9.9 + - - +
1096G LYS* 3.4 58.0 - - + +
1097G ILE* 3.9 16.8 - - + -
1098G PRO* 4.1 6.7 - - + +
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Residues in contact with GLY1091 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086G LEU 3.2 1.4 + - - -
1087G HIS 3.6 10.1 + - - -
1088G GLN 4.8 0.8 + - - -
1089G TYR 3.8 0.6 - - - -
1090G TYR* 1.3 78.8 - - - +
1092G ASP* 1.3 64.0 + - - +
1093G ASP* 2.6 19.4 + - - +
1096G LYS* 5.4 1.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il