Contacts of the helix formed by residues 1103 - 1113 (chain M) in PDB entry 6G0L
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 ASN1103 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085M TYR* 3.2 41.9 + - + -
1100M PRO* 2.7 25.5 + - + +
1101M LYS 3.4 0.8 + - - +
1102M ASP* 1.3 76.6 + - - +
1104M PRO* 1.3 74.7 - - + +
1105M LEU* 4.1 11.3 - - - +
1106M THR* 2.6 60.1 + - - +
1107M ARG* 3.4 11.7 + - - +
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Residues in contact with PRO1104 (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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1078M LEU* 4.6 4.2 - - + +
1081M HIS* 3.5 30.5 - - + +
1082M ALA* 3.7 26.0 - - + +
1085M TYR* 3.8 19.5 - - + -
1103M ASN* 1.3 88.2 - - + +
1105M LEU* 1.3 56.7 + - - +
1107M ARG* 3.4 18.6 - - + +
1108M LEU* 2.9 31.9 + - - +
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Residues in contact with LEU1105 (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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1082M ALA* 4.1 22.7 - - + +
1085M TYR* 3.8 31.9 - - + -
1086M ARG* 4.3 21.3 - - + -
1089M LEU* 4.4 13.7 - - + -
1103M ASN* 3.1 9.8 + - - +
1104M PRO* 1.3 77.5 - - - +
1106M THR* 1.3 59.0 + - + +
1108M LEU* 3.4 7.8 + - + +
1109M SER* 2.9 29.6 + - - -
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Residues in contact with THR1106 (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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1100M PRO 4.9 0.4 - - - +
1101M LYS* 2.6 32.8 + - + +
1102M ASP* 4.4 0.2 - - - -
1103M ASN* 2.6 37.7 + - - +
1105M LEU* 1.3 77.2 - - + +
1107M ARG* 1.3 55.0 + - - +
1109M SER* 3.3 6.1 + - - -
1110M LEU* 2.9 40.5 + - - +
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Residues in contact with ARG1107 (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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1078M LEU* 3.8 27.7 - - + +
1081M HIS* 5.5 6.6 + - - -
1102M ASP* 6.1 1.3 - - - -
1103M ASN 3.7 5.2 - - - +
1104M PRO* 3.4 27.8 - - + +
1106M THR* 1.3 81.1 + - - +
1108M LEU* 1.3 58.2 + - - +
1110M LEU* 3.8 9.6 - - - +
1111M LYS* 2.9 26.9 + - - +
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Residues in contact with LEU1108 (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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1075M LEU* 4.4 18.6 - - + +
1078M LEU* 3.7 36.1 - - + +
1079M GLU* 5.1 10.1 - - + -
1082M ALA* 4.2 22.2 - - + -
1104M PRO 2.9 20.2 + - - +
1105M LEU* 3.7 8.5 - - + +
1107M ARG* 1.3 76.5 - - - +
1109M SER* 1.3 60.0 + - - +
1111M LYS* 3.0 5.2 + - + +
1112M LYS* 2.9 54.9 + - + +
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Residues in contact with SER1109 (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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-82J A 5.5 2.6 + - - -
1105M LEU 2.9 17.0 + - - -
1106M THR* 3.7 6.5 - - - -
1108M LEU* 1.3 75.0 - - - +
1110M LEU* 1.3 64.3 + - - +
1112M LYS* 3.2 21.5 + - - +
1113M ARG* 3.2 30.3 + - - +
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Residues in contact with LEU1110 (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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1106M THR* 2.9 26.6 + - - +
1107M ARG* 4.1 7.2 - - - +
1109M SER* 1.3 75.3 - - - +
1111M LYS* 1.3 64.6 + - - +
1113M ARG* 3.2 26.1 - - + +
1114M GLU* 3.1 22.2 + - - +
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Residues in contact with LYS1111 (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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1071M ARG* 3.5 28.2 - - - +
1074M ILE* 3.9 27.1 - - + -
1075M LEU* 3.8 19.4 - - + +
1078M LEU* 3.7 22.9 - - + -
1107M ARG 2.9 21.2 + - - +
1108M LEU* 3.0 8.4 + - + +
1110M LEU* 1.3 73.9 - - - +
1112M LYS* 1.3 63.9 + - - +
1114M GLU* 2.8 51.7 + - + +
1116M LYS* 4.8 8.9 - - - +
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Residues in contact with LYS1112 (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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-82J A 3.7 38.3 + - - +
1075M LEU* 5.8 6.6 - - + +
1108M LEU* 2.9 45.1 + - + +
1109M SER* 3.2 13.7 + - - +
1111M LYS* 1.3 79.1 - - - +
1113M ARG* 1.3 56.9 + - - +
1114M GLU* 3.3 6.6 + - - +
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Residues in contact with ARG1113 (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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79I T 5.6 10.2 - - - +
-83J C 6.1 2.0 - - - +
-82J A 5.5 14.5 + - - -
1109M SER* 3.2 25.9 + - - +
1110M LEU* 3.2 29.2 - - + +
1112M LYS* 1.3 75.8 - - + +
1114M GLU* 1.3 64.6 + - - +
1115M LYS* 3.6 17.1 + - - +
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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