Contacts of the helix formed by residues 1059 - 1073 (chain M) in PDB entry 4G7Z
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 ASP1059 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054M THR* 3.0 29.9 + - - +
1055M LEU* 3.8 3.5 - - - +
1058M ASP* 1.3 77.4 + - - +
1060M ILE* 1.3 61.0 + - - +
1061M GLU* 3.5 2.4 + - - +
1062M GLY* 3.1 20.7 + - - -
1063M ARG* 3.1 29.8 + - - +
1079M PRO* 3.8 4.9 - - - +
1080M SER* 2.6 51.5 + - - +
1081M VAL 3.7 9.0 - - - +
1082M PRO* 4.2 9.4 - - + -
1086M ARG* 5.7 0.2 + - - -
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Residues in contact with ILE1060 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018M GLN* 3.7 6.5 - - + -
1058M ASP 3.1 14.8 + - - +
1059M ASP* 1.3 72.5 + - - +
1061M GLU* 1.3 64.8 + - - +
1063M ARG* 3.3 26.9 - - - +
1064M ASN* 3.0 42.6 + - - +
1081M VAL 5.1 1.0 + - - -
1083M GLU* 3.6 35.4 + - + +
84N ILE* 4.4 10.8 - - + -
87N ARG* 5.1 0.2 - - - +
338P LEU* 3.6 42.2 - - + -
339P PRO 5.6 0.9 - - - +
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Residues in contact with GLU1061 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059M ASP* 3.5 1.7 + - - +
1060M ILE* 1.3 80.6 - - - +
1062M GLY* 1.3 60.1 + - - +
1064M ASN* 4.2 5.3 - - - +
1065M ALA* 3.1 29.8 + - + +
1078M GLU 5.6 1.4 - - - +
1080M SER* 3.6 24.2 + - - +
1086M ARG* 5.9 0.3 + - - -
1113M GLU* 4.5 15.1 - - - +
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Residues in contact with GLY1062 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055M LEU* 3.5 18.9 - - - +
1059M ASP* 3.1 27.4 + - - -
1061M GLU* 1.3 80.6 - - - +
1063M ARG* 1.3 52.1 + - - +
1065M ALA* 3.6 3.2 - - - +
1066M ALA* 2.7 36.7 + - - +
1077M PRO* 4.3 1.7 - - - +
1078M GLU 5.3 2.2 - - - -
1079M PRO* 5.2 0.4 - - - -
1080M SER* 3.6 4.0 + - - -
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Residues in contact with ARG1063 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013M TYR* 3.5 41.2 - - - -
1018M GLN* 2.7 56.0 + - - +
1055M LEU* 3.1 25.6 + - - +
1057M SER 2.8 17.0 + - - -
1058M ASP* 3.9 5.9 - - - +
1059M ASP 3.1 19.7 + - - +
1060M ILE* 3.3 31.5 - - - +
1062M GLY* 1.3 73.9 - - - +
1064M ASN* 1.3 76.7 + - - +
1066M ALA* 3.9 3.4 - - - +
1067M TYR* 3.1 25.3 + - - +
624N ASP* 4.3 6.1 - - - +
338P LEU* 4.5 4.9 - - - +
339P PRO 5.4 3.6 + - - -
341P PRO* 3.7 7.7 - - + +
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Residues in contact with ASN1064 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060M ILE* 3.0 34.2 + - - +
1061M GLU* 4.2 4.1 - - - +
1063M ARG* 1.3 82.7 + - - +
1065M ALA* 1.3 58.2 + - - +
1067M TYR* 4.1 1.7 - - - +
1068M GLU* 3.2 29.7 + - - +
338P LEU* 5.4 2.4 - - - +
339P PRO* 3.9 12.6 + - - +
341P PRO* 3.1 41.3 - - - +
344P ALA* 4.1 20.6 - - + +
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Residues in contact with ALA1065 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061M GLU* 3.1 24.0 + - + +
1062M GLY* 3.9 1.3 - - - +
1064M ASN* 1.3 77.0 - - - +
1066M ALA* 1.3 59.3 + - - +
1068M GLU* 3.8 7.5 - - - +
1069M ALA* 3.0 28.2 + - - +
1077M PRO* 3.6 20.8 - - + +
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Residues in contact with ALA1066 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055M LEU* 4.3 21.1 - - + +
1062M GLY 2.7 23.5 + - - +
1063M ARG* 3.9 6.1 - - - +
1064M ASN 3.4 0.2 - - - -
1065M ALA* 1.3 71.5 - - - +
1067M TYR* 1.3 66.2 + - - +
1069M ALA* 3.2 2.6 + - - +
1070M ILE* 3.0 30.6 + - + +
1076M VAL* 4.5 7.1 - - + +
1077M PRO* 3.7 16.5 - - + +
625N TYR* 5.3 3.4 - - + +
751N LEU* 5.2 7.6 - - + -
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Residues in contact with TYR1067 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009M SER* 6.0 0.7 - - - -
1010M THR* 4.5 13.7 - - + -
1063M ARG 3.1 16.0 + - - +
1066M ALA* 1.3 79.8 - - - +
1068M GLU* 1.3 58.1 + - - +
1070M ILE* 4.0 2.5 - - - +
1071M ILE* 2.9 67.6 + - + +
625N TYR* 3.9 15.8 + - - +
655N PRO* 3.7 25.4 - - + -
658N LEU* 3.8 2.8 - - - +
670N VAL* 5.0 2.4 - - - +
674N ARG* 2.8 34.7 + - - -
341P PRO* 3.5 29.6 - - + -
342P VAL* 3.8 30.0 - - + +
345P ALA* 4.0 11.2 - - + -
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Residues in contact with GLU1068 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064M ASN 3.2 18.1 + - - +
1065M ALA* 4.0 7.3 - - - +
1066M ALA 3.3 0.2 - - - -
1067M TYR* 1.3 81.1 - - - +
1069M ALA* 1.3 57.0 + - - +
1071M ILE* 4.1 6.5 - - + +
1072M LYS* 3.0 60.1 + - + +
1074M GLU* 5.2 0.2 - - - -
344P ALA* 4.3 5.4 - - - +
345P ALA* 4.0 23.5 + - + -
348P SER* 3.2 21.9 + - - -
352P GLU* 4.6 1.0 - - - +
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Residues in contact with ALA1069 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065M ALA 3.0 19.7 + - - +
1066M ALA 3.5 4.7 - - - +
1067M TYR 3.1 0.2 - - - -
1068M GLU* 1.3 77.2 - - - +
1070M ILE* 1.3 58.3 + - + +
1072M LYS 3.5 0.9 + - - -
1073M GLY 2.8 7.4 + - - -
1074M GLU* 2.4 60.8 + - + +
1075M ASP 4.1 4.0 - - - +
1076M VAL* 4.3 2.0 - - - -
1077M PRO* 3.8 17.9 - - + -
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Residues in contact with ILE1070 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066M ALA 3.0 17.5 + - - +
1067M TYR 4.0 2.9 - - - +
1069M ALA* 1.3 74.3 - - - +
1071M ILE* 1.3 66.8 + - - +
1073M GLY* 3.2 11.2 + - - +
1074M GLU 4.3 3.4 - - - +
1076M VAL* 3.8 26.7 - - + -
625N TYR* 4.6 12.8 - - + +
655N PRO* 3.5 27.9 - - + +
656N PHE* 3.6 54.2 - - + +
659N LYS* 3.9 5.9 - - - +
751N LEU* 4.5 16.6 - - + -
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Residues in contact with ILE1071 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067M TYR* 2.9 67.7 + - + +
1068M GLU* 4.1 7.0 - - + +
1070M ILE* 1.3 78.5 - - - +
1072M LYS* 1.3 63.5 + - + +
655N PRO* 3.7 17.3 - - + +
658N LEU* 3.6 22.7 - - + -
659N LYS* 3.2 26.2 - - - +
662N GLU* 4.7 0.5 - - - +
670N VAL* 3.6 33.8 - - + +
345P ALA* 5.4 3.6 - - + -
349P LEU* 5.0 10.8 - - + -
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Residues in contact with LYS1072 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068M GLU* 3.0 51.2 + - + +
1069M ALA 4.0 2.7 - - - +
1071M ILE* 1.3 83.8 - - + +
1073M GLY* 1.3 60.9 + - - +
1074M GLU* 3.9 29.5 - - - +
659N LYS* 3.7 14.9 - - - -
345P ALA* 6.1 0.2 - - - +
348P SER* 4.4 2.0 + - - -
349P LEU* 4.6 11.8 - - + +
352P GLU* 3.4 31.3 + - - -
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Residues in contact with GLY1073 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069M ALA 2.8 6.5 + - - -
1070M ILE* 3.2 9.8 + - - -
1071M ILE 3.2 5.1 + - - -
1072M LYS* 1.3 80.4 - - - +
1074M GLU* 1.3 59.6 + - - +
659N LYS* 4.3 13.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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