Contacts of the helix formed by residues 1121 - 1131 (chain B) in PDB entry 4E5W
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 PRO1121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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977B LEU* 3.7 32.1 - - + -
1119B ASN 3.6 8.0 - - - +
1120B CYS* 1.4 91.3 - - - +
1122B ASP* 1.3 65.8 + - - +
1123B GLU* 3.6 27.6 - - + +
1124B VAL* 3.0 23.8 + - + -
1125B TYR* 3.1 9.8 + - - +
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Residues in contact with ASP1122 (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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1116B CYS* 5.3 2.4 - - - -
1120B CYS 3.7 1.8 + - - -
1121B PRO* 1.3 70.9 - - - +
1123B GLU* 1.4 57.3 + - - +
1125B TYR* 3.2 12.6 + - - -
1126B GLN* 2.8 67.3 + - - +
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Residues in contact with GLU1123 (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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1121B PRO* 3.6 24.5 - - + +
1122B ASP* 1.4 81.8 + - - +
1124B VAL* 1.4 63.7 + - + +
1126B GLN* 3.8 7.4 + - - +
1127B LEU* 3.6 24.6 + - - +
1152B LEU* 3.7 32.2 - - + +
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Residues in contact with VAL1124 (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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977B LEU* 4.5 3.6 - - + -
981B LEU* 3.9 33.2 - - + -
1071B LEU* 4.7 5.1 - - + +
1075B LEU* 3.9 17.9 - - + -
1120B CYS* 3.7 17.3 - - - -
1121B PRO* 3.0 30.1 + - + +
1123B GLU* 1.4 75.0 - - + +
1125B TYR* 1.3 65.8 + - - +
1127B LEU* 3.1 16.7 + - - +
1128B MET* 3.2 11.9 + - + +
1149B PHE* 4.7 7.9 - - + -
1152B LEU* 3.9 21.3 - - + -
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Residues in contact with TYR1125 (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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1113B ARG 4.9 0.2 + - - -
1114B LEU 2.7 26.0 + - - -
1115B PRO* 3.8 2.9 - - - +
1116B CYS* 3.6 58.2 + - + -
1117B PRO* 4.3 1.6 - - + -
1120B CYS* 3.9 4.2 - - - -
1121B PRO 3.1 7.4 + - - +
1122B ASP* 3.6 13.2 - - - +
1124B VAL* 1.3 76.7 - - - +
1126B GLN* 1.3 69.5 + - - +
1128B MET* 3.2 29.9 + - - +
1129B ARG* 2.8 68.8 + - + +
1132B TRP* 4.3 2.3 - + - -
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Residues in contact with GLN1126 (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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1122B ASP* 2.8 52.1 + - - +
1123B GLU* 4.1 8.7 - - - +
1124B VAL 3.3 0.2 - - - -
1125B TYR* 1.3 82.8 - - - +
1127B LEU* 1.4 63.1 + - - +
1129B ARG* 3.4 21.4 + - - +
1130B LYS* 3.2 31.8 + - - +
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Residues in contact with LEU1127 (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 LEU* 5.2 0.4 - - - -
1123B GLU 3.6 7.7 + - - +
1124B VAL 3.1 9.0 + - - +
1126B GLN* 1.4 73.1 - - - +
1128B MET* 1.3 64.7 + - - +
1130B LYS* 3.3 32.8 + - + +
1131B CYS* 3.6 11.3 + - - -
1144B ASN* 4.9 6.7 - - - +
1145B LEU* 3.8 28.3 - - + +
1148B GLY* 3.8 38.4 - - - -
1149B PHE* 3.9 22.2 - - + +
1152B LEU* 3.9 22.4 - - + -
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Residues in contact with MET1128 (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 GLY 3.6 13.0 - - - +
1071B LEU* 4.0 16.5 - - + +
1072B HIS* 3.8 30.1 - - - +
1075B LEU* 3.5 31.9 - - + -
1117B PRO* 4.1 11.2 - - + -
1124B VAL 3.2 10.4 + - - +
1125B TYR* 3.3 28.7 - - + +
1127B LEU* 1.3 76.1 - - - +
1129B ARG* 1.4 55.9 + - - +
1131B CYS* 3.1 29.7 + - - +
1132B TRP* 3.4 38.8 - - + -
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Residues in contact with ARG1129 (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 GLY 4.3 9.7 + - - -
1113B ARG* 3.9 29.9 + - - +
1125B TYR* 2.8 65.0 + - + +
1126B GLN* 3.7 26.9 - - - +
1127B LEU 3.3 0.4 - - - -
1128B MET* 1.4 74.9 - - - +
1130B LYS* 1.3 56.3 + - + +
1132B TRP* 3.0 36.5 + - + +
1133B GLU* 3.8 5.2 + - - +
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Residues in contact with LYS1130 (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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1126B GLN* 3.2 20.2 + - - +
1127B LEU* 3.3 23.7 + - + +
1129B ARG* 1.3 73.8 - - + +
1131B CYS* 1.4 60.1 + - - +
1132B TRP 3.2 0.4 + - - -
1133B GLU* 4.1 10.0 + - - +
1138B ASN 4.5 0.4 - - - +
1139B ARG* 3.4 9.2 - - - +
1140B THR* 3.1 43.2 + - + +
1144B ASN* 4.7 9.4 - - - +
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Residues in contact with CYS1131 (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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1064B VAL* 3.4 33.7 - - - +
1065B TRP* 3.3 14.0 - - - +
1067B PHE* 4.0 4.5 - - - -
1068B GLY* 3.8 20.2 - - - -
1127B LEU 3.7 15.3 - - - -
1128B MET* 3.1 15.0 + - - +
1130B LYS* 1.4 75.5 - - - +
1132B TRP* 1.3 58.5 + - + +
1133B GLU 3.6 0.9 - - - -
1139B ARG* 3.2 21.6 - - - -
1140B THR* 4.0 0.7 - - - -
1145B LEU* 3.8 29.6 - - - -
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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