Contacts of the helix formed by residues 1059 - 1073 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1054C THR* 2.9 30.4 + - - +
1055C LEU* 3.5 9.7 - - - +
1057C SER 3.6 0.2 - - - -
1058C ASP* 1.3 76.2 + - - +
1060C ILE* 1.3 60.2 + - - +
1061C GLU* 3.8 1.2 + - - +
1062C GLY* 3.0 23.8 + - - -
1063C ARG* 3.0 29.3 + - - +
1079C PRO* 3.7 1.7 - - - +
1080C SER* 2.2 47.8 + - - +
1081C VAL 3.5 10.3 - - - +
1082C PRO* 4.0 10.1 - - + -
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Residues in contact with ILE1060 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018C GLN* 3.5 30.1 - - + -
1058C ASP 3.1 14.6 - - - +
1059C ASP* 1.3 70.3 + - - +
1061C GLU* 1.3 67.2 + - - +
1063C ARG* 3.0 31.8 - - - +
1064C ASN* 3.0 39.6 + - - +
1081C VAL 4.9 0.6 + - - -
1083C GLU* 3.6 25.5 - - + +
1086C ARG* 5.9 1.6 - - - +
84D ILE* 5.6 3.1 - - + -
87D ARG* 5.1 0.4 - - - +
338F LEU* 4.1 28.0 - - + -
339F PRO 5.6 1.3 - - - +
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Residues in contact with GLU1061 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059C ASP* 3.8 0.6 + - - -
1060C ILE* 1.3 78.6 - - - +
1062C GLY* 1.3 63.1 + - - +
1064C ASN* 4.1 7.8 - - - +
1065C ALA* 3.2 29.6 + - + +
1078C GLU 5.3 3.5 - - - +
1080C SER* 3.9 23.3 + - - +
1113C GLU* 4.2 16.8 - - - +
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Residues in contact with GLY1062 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055C LEU* 3.2 17.2 - - - +
1059C ASP* 3.0 27.7 + - - -
1060C ILE 3.1 1.2 - - - -
1061C GLU* 1.3 83.3 - - - +
1063C ARG* 1.3 49.7 + - - +
1065C ALA* 3.6 2.3 - - - -
1066C ALA* 2.6 34.8 + - - +
1077C PRO* 3.9 4.9 - - - +
1078C GLU 5.7 0.9 - - - -
1079C PRO* 5.1 0.7 - - - -
1080C SER* 3.7 4.2 + - - -
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Residues in contact with ARG1063 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013C TYR* 3.4 41.6 - - - -
1018C GLN* 2.7 51.9 + - - +
1055C LEU 3.0 24.7 + - - +
1057C SER 2.9 20.4 + - - -
1058C ASP* 4.0 2.8 - - - +
1059C ASP 3.0 12.1 + - - +
1060C ILE* 3.0 43.2 + - - +
1062C GLY* 1.3 71.8 - - - +
1064C ASN* 1.3 67.3 + - - +
1065C ALA 3.2 1.3 - - - -
1066C ALA* 3.7 5.5 - - - +
1067C TYR* 3.3 16.1 + - - +
624D ASP* 4.4 7.6 - - - +
338F LEU* 5.4 2.8 + - - +
339F PRO 5.3 5.3 + - - -
340F SER* 6.0 0.2 - - - +
341F PRO* 3.5 21.5 - - + +
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Residues in contact with ASN1064 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060C ILE* 3.0 35.7 + - - +
1061C GLU* 4.1 6.6 - - - +
1063C ARG* 1.3 81.2 + - - +
1065C ALA* 1.3 58.4 + - - +
1067C TYR* 4.3 0.5 - - - +
1068C GLU* 3.3 28.9 + - - +
338F LEU* 5.4 3.2 - - - +
339F PRO* 3.6 14.1 + - - +
340F SER 3.7 0.2 - - - -
341F PRO* 3.1 40.1 - - - +
344F ALA* 4.0 20.3 - - + +
345F ALA 5.0 0.7 + - - -
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Residues in contact with ALA1065 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C GLU* 3.2 20.3 + - + +
1062C GLY* 4.0 2.5 - - - +
1064C ASN* 1.3 78.6 - - - +
1066C ALA* 1.3 59.0 + - - +
1067C TYR 3.4 0.7 - - - -
1068C GLU* 3.8 9.6 - - - +
1069C ALA* 3.0 28.9 + - - +
1077C PRO* 3.6 16.7 - - + +
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Residues in contact with ALA1066 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055C LEU* 4.1 24.7 - - + +
1062C GLY 2.6 23.4 + - - +
1063C ARG* 3.8 10.3 - - - +
1064C ASN 3.5 0.2 - - - -
1065C ALA* 1.3 74.0 - - - +
1067C TYR* 1.3 61.4 + - - +
1069C ALA* 3.2 13.2 + - - +
1070C ILE* 3.2 23.7 + - + +
1076C VAL* 5.3 3.4 - - + +
1077C PRO* 3.7 11.4 - - + -
625D TYR* 5.4 4.7 - - + +
751D LEU* 5.8 6.1 - - + -
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Residues in contact with TYR1067 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009C SER* 6.1 0.2 - - - -
1010C THR* 4.4 11.0 - - + -
1063C ARG 3.3 16.6 + - - +
1064C ASN 4.3 0.4 - - - +
1066C ALA* 1.3 74.9 - - - +
1068C GLU* 1.3 65.2 + - - +
1070C ILE* 3.5 5.0 + - - +
1071C ILE* 3.1 48.7 + - + +
625D TYR* 4.1 16.5 + - - +
655D PRO* 3.7 27.8 - - + -
658D LEU* 3.9 0.7 - - - +
670D VAL* 4.6 3.9 - - + +
674D ARG* 3.0 47.5 + - - -
341F PRO* 3.6 17.5 - - + -
342F VAL* 3.9 14.1 - - + +
345F ALA* 3.3 33.2 - - + -
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Residues in contact with GLU1068 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064C ASN* 3.3 19.6 + - - +
1065C ALA* 3.8 9.5 - - - +
1066C ALA 3.3 0.2 - - - -
1067C TYR* 1.3 83.1 - - - +
1069C ALA* 1.3 63.6 + - - +
1071C ILE* 3.6 4.7 - - + +
1072C LYS* 3.1 54.1 + - + +
1074C GLU* 5.6 0.4 - - - +
344F ALA* 3.9 5.0 - - - +
345F ALA* 3.7 20.7 + - + -
348F SER* 2.4 36.3 + - - -
349F LEU* 5.9 1.3 - - + -
352F GLU* 4.1 0.9 - - - +
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Residues in contact with ALA1069 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065C ALA 3.0 20.6 + - - +
1066C ALA 3.4 6.3 - - - +
1068C GLU* 1.3 78.0 - - - +
1070C ILE* 1.3 56.4 + - + +
1072C LYS 3.9 0.2 + - - -
1073C GLY 3.3 1.9 + - - -
1074C GLU* 2.5 53.4 + - - +
1075C ASP 3.9 14.8 - - - +
1076C VAL* 4.3 2.5 - - - -
1077C PRO* 3.7 17.7 - - + -
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Residues in contact with ILE1070 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066C ALA* 3.2 18.3 + - + +
1067C TYR* 3.5 2.2 + - - +
1068C GLU 3.3 0.4 - - - -
1069C ALA* 1.3 75.9 - - - +
1071C ILE* 1.3 61.9 + - - +
1073C GLY* 3.0 17.9 + - - +
1074C GLU 4.4 5.4 - - - +
1076C VAL* 4.9 12.8 - - + -
625D TYR* 4.5 11.4 - - + +
655D PRO* 3.7 14.6 - - + -
656D PHE* 3.5 71.3 - - + +
659D LYS* 3.8 9.4 - - - +
751D LEU* 4.1 20.2 - - + -
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Residues in contact with ILE1071 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067C TYR* 3.1 55.4 - - + +
1068C GLU* 3.6 7.0 - - + +
1070C ILE* 1.3 76.2 - - - +
1072C LYS* 1.3 69.4 + - + +
1073C GLY 3.3 0.3 + - - -
655D PRO* 3.9 14.8 - - + +
658D LEU* 3.7 16.8 - - + -
659D LYS* 3.3 24.5 - - - +
662D GLU* 5.1 0.3 - - - +
670D VAL* 3.5 46.7 - - + +
345F ALA* 5.8 1.1 - - + -
349F LEU* 4.5 15.7 - - + -
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Residues in contact with LYS1072 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C GLU* 3.1 42.4 + - + +
1069C ALA 4.0 0.4 - - - +
1071C ILE* 1.3 84.0 - - + +
1073C GLY* 1.3 60.6 + - - +
1074C GLU* 3.0 41.4 - - + +
659D LYS* 3.9 14.2 - - - -
348F SER* 4.1 2.0 + - - -
349F LEU* 4.3 12.2 - - + +
352F GLU* 2.6 39.0 + - - -
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Residues in contact with GLY1073 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069C ALA 3.3 0.2 + - - -
1070C ILE 3.0 17.6 + - - -
1071C ILE 3.1 0.6 + - - -
1072C LYS* 1.3 80.5 - - - +
1074C GLU* 1.3 63.8 + - - +
659D LYS* 4.2 12.3 - - - -
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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