Contacts of the helix formed by residues 1101 - 1115 (chain B) in PDB entry 1G24
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 PRO1101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089B LYS* 4.4 15.3 - - - +
1099B GLY 3.9 1.5 - - - +
1100B PHE* 1.3 89.7 - - + +
1102B SER* 1.3 67.0 + - - +
1103B ASN* 4.5 5.8 - - + +
1104B LEU* 3.0 31.3 + - + +
1105B ILE* 3.0 10.9 + - - +
2044C ASN* 4.7 4.5 - - - +
2123C ASN* 5.9 0.7 - - - +
2196C LYS* 4.4 2.5 - - - +
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Residues in contact with SER1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B PHE 3.5 2.3 + - - -
1101B PRO* 1.3 71.7 - - - +
1103B ASN* 1.3 66.0 + - - +
1105B ILE* 3.3 11.2 + - - +
1106B LYS* 3.0 23.6 + - - +
2196C LYS* 3.6 23.1 - - - +
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Residues in contact with ASN1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101B PRO* 3.2 4.7 - - + +
1102B SER* 1.3 78.7 - - - +
1104B LEU* 1.3 57.9 + - - +
1106B LYS* 3.3 13.7 + - - +
1107B GLN* 3.0 40.4 + - - +
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Residues in contact with LEU1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086B ILE* 4.0 29.4 - - + -
1089B LYS* 3.7 35.2 - - + +
1100B PHE* 3.6 32.8 - - + -
1101B PRO* 3.0 20.2 + - + +
1103B ASN* 1.3 77.2 - - - +
1105B ILE* 1.3 60.3 + - - +
1107B GLN* 3.1 20.4 + - + +
1108B VAL* 2.8 45.1 + - + +
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Residues in contact with ILE1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097B ILE* 3.4 32.8 - - + +
1098B ASN* 3.8 14.1 - - - +
1100B PHE* 3.4 22.7 - - + +
1101B PRO 3.0 14.2 + - - +
1102B SER* 3.6 9.9 - - - +
1104B LEU* 1.3 75.3 - - - +
1106B LYS* 1.3 64.8 + - - +
1108B VAL* 3.3 5.4 + - - +
1109B GLU* 2.9 54.5 + - + +
2196C LYS* 4.0 12.1 - - - -
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Residues in contact with LYS1106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071B SER* 4.9 7.5 - - - -
1102B SER 3.0 13.2 + - - +
1103B ASN* 3.4 15.9 - - - +
1105B ILE* 1.3 80.8 - - - +
1107B GLN* 1.3 64.4 + - + +
1109B GLU* 3.6 5.7 + - - +
1110B LEU* 3.1 48.9 + - + +
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Residues in contact with GLN1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075B ALA* 3.8 14.9 - - + +
1078B SER* 3.4 32.5 + - - -
1086B ILE* 5.0 5.7 - - + +
1103B ASN* 3.0 22.5 + - - +
1104B LEU* 3.1 25.8 + - + +
1106B LYS* 1.3 77.0 - - + +
1108B VAL* 1.3 60.4 + - + +
1110B LEU* 3.2 10.3 + - + +
1111B LEU* 2.9 38.2 + - + +
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Residues in contact with VAL1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086B ILE* 4.7 13.2 - - + -
1090B LEU* 5.1 1.8 - - + -
1097B ILE* 4.1 14.8 - - + -
1100B PHE* 4.6 12.8 - - + -
1104B LEU* 2.8 43.1 + - + +
1105B ILE 3.8 3.8 - - - +
1107B GLN* 1.3 72.4 - - + +
1109B GLU* 1.3 56.7 + - - +
1111B LEU* 3.1 5.2 + - + -
1112B ASP* 2.8 46.1 + - - +
1172B TYR* 3.3 22.3 + - + +
1219B ARG* 3.5 20.0 - - - +
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Residues in contact with GLU1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097B ILE* 3.9 22.7 - - + +
1105B ILE* 2.9 30.9 + - - +
1106B LYS* 4.1 4.2 - - - +
1108B VAL* 1.3 76.3 - - - +
1110B LEU* 1.3 62.4 + - - +
1112B ASP* 3.7 10.2 - - - +
1113B LYS* 3.1 26.0 + - - +
1250B PRO* 5.4 0.3 - - - +
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Residues in contact with LEU1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071B SER* 3.8 37.9 - - - +
1072B GLU* 4.3 17.6 - - + +
1075B ALA* 3.8 14.4 - - + -
1106B LYS* 3.1 49.7 + - + +
1107B GLN* 3.5 10.3 - - + +
1108B VAL 3.1 0.2 - - - -
1109B GLU* 1.3 74.7 - - - +
1111B LEU* 1.3 59.9 + - - +
1113B LYS* 3.4 9.3 + - + +
1114B SER* 2.9 30.2 + - - -
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Residues in contact with LEU1111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072B GLU 5.9 0.2 - - - -
1075B ALA* 3.4 34.5 - - + +
1076B ILE* 3.5 22.9 - - + +
1079B TYR* 4.1 22.7 - - + -
1086B ILE* 5.3 5.4 - - + -
1107B GLN* 2.9 22.6 + - + +
1108B VAL* 3.5 11.0 - - + +
1110B LEU* 1.3 77.4 - - - +
1112B ASP* 1.3 64.2 + - - +
1114B SER* 2.7 24.4 + - - +
1115B PHE* 3.3 14.0 - - + -
1172B TYR* 3.6 33.9 - - + +
1216B LEU* 5.1 7.6 - - + -
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Residues in contact with ASP1112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108B VAL* 2.8 26.4 + - - +
1109B GLU* 3.7 10.9 - - - +
1111B LEU* 1.3 74.6 - - - +
1113B LYS* 1.3 60.7 + - - +
1115B PHE* 3.5 22.0 + - - +
1116B ASN* 4.7 1.7 + - - +
1172B TYR* 2.8 25.5 + - - -
1199B LYS* 5.1 0.9 + - - -
1218B PRO* 6.1 1.0 - - - +
1219B ARG* 2.9 40.2 + - - +
1248B ILE* 3.5 25.7 - - + +
1250B PRO* 3.9 15.5 - - + +
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Residues in contact with LYS1113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072B GLU* 4.4 11.4 - - - +
1109B GLU 3.1 18.3 + - - +
1110B LEU* 4.0 8.1 - - + +
1112B ASP* 1.3 73.5 - - - +
1114B SER* 1.3 64.2 + - - +
1115B PHE 3.0 2.7 - - - -
1116B ASN* 3.0 31.7 + - + +
1117B LYS* 4.4 1.7 + - - +
1250B PRO* 3.7 19.7 - - + +
1251B LYS 3.8 25.9 - - - -
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Residues in contact with SER1114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068B LEU* 4.2 11.7 - - - +
1072B GLU* 3.7 25.8 + - - -
1076B ILE* 4.5 8.1 - - - +
1110B LEU 2.9 16.3 + - - -
1111B LEU* 2.7 21.8 + - - +
1113B LYS* 1.3 76.8 - - - +
1115B PHE* 1.3 58.4 + - - +
1117B LYS* 3.0 23.8 + - - +
1118B MET* 3.2 31.2 + - - +
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Residues in contact with PHE1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1111B LEU* 3.3 25.8 - - + -
1112B ASP* 3.5 15.2 + - - +
1113B LYS 3.0 1.2 - - - -
1114B SER* 1.3 76.4 + - - +
1116B ASN* 1.3 60.5 + - - +
1117B LYS 2.9 7.3 + - - -
1118B MET* 3.1 29.1 + - + +
1119B LYS* 3.1 16.7 + - - -
1172B TYR* 4.3 13.5 - + - -
1199B LYS* 3.7 35.4 - - + +
1200B ALA* 4.0 6.3 - - - -
1201B GLY 4.0 7.0 - - - -
1216B LEU* 3.2 42.2 - - + -
1217B LEU 3.6 6.1 - - - -
1218B PRO* 3.5 38.1 - - + -
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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