Contacts of the helix formed by residues 1141 - 1153 (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 SER1141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1064B VAL* 4.6 4.3 - - - -
1139B ARG 3.9 0.2 + - - -
1140B THR* 1.3 87.5 + - - +
1142B PHE* 1.4 64.2 + - - +
1143B GLN* 3.5 8.7 + - - +
1144B ASN* 3.0 25.0 + - - +
1145B LEU* 3.2 15.5 + - - +
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Residues in contact with PHE1142 (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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988B CYS* 3.8 37.4 - - - +
991B MET* 3.6 47.3 - - + -
992B ASP* 3.8 18.0 + - + +
995B GLY* 6.4 0.2 - - - -
1060B ILE* 4.5 13.2 - - + -
1063B ASP* 3.8 26.0 - - + -
1064B VAL* 3.6 24.6 - - + +
1067B PHE* 3.6 27.6 - + + -
1141B SER* 1.4 72.4 - - - +
1143B GLN* 1.4 63.1 + - - +
1145B LEU* 3.2 9.5 + - + +
1146B ILE* 3.0 29.0 + - - +
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Residues in contact with GLN1143 (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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992B ASP* 3.6 24.0 + - - +
1141B SER* 3.3 7.9 + - - +
1142B PHE* 1.4 78.5 - - - +
1144B ASN* 1.4 59.4 + - - +
1146B ILE* 3.4 26.0 + - - +
1147B GLU* 3.2 41.3 + - - +
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Residues in contact with ASN1144 (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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1127B LEU* 4.9 5.5 - - - +
1130B LYS* 4.7 10.9 - - - +
1140B THR* 2.9 26.1 + - - +
1141B SER* 3.0 17.4 + - - +
1143B GLN* 1.4 72.4 - - - +
1145B LEU* 1.4 60.1 + - - +
1147B GLU* 3.4 15.7 + - - +
1148B GLY* 3.0 24.4 + - - -
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Residues in contact with LEU1145 (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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988B CYS* 3.9 15.7 - - - -
1064B VAL* 4.2 5.4 - - + -
1067B PHE* 3.7 25.6 - - + -
1071B LEU* 5.8 0.2 - - + -
1127B LEU* 3.8 37.6 - - + +
1131B CYS* 3.8 13.9 - - - -
1140B THR* 3.7 16.6 + - + +
1141B SER 3.2 19.2 + - - +
1142B PHE* 3.2 16.6 + - + +
1144B ASN* 1.4 73.2 - - - +
1146B ILE* 1.3 58.7 + - - +
1148B GLY* 3.2 1.8 + - - +
1149B PHE* 2.9 57.0 + - + -
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Residues in contact with ILE1146 (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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985B VAL* 4.2 13.4 - - + +
988B CYS* 3.6 20.9 - - + +
989B LYS* 3.8 43.5 - - + +
992B ASP* 4.7 4.9 - - + -
1142B PHE 3.0 24.8 + - - +
1143B GLN* 3.6 28.7 - - - +
1145B LEU* 1.3 73.8 - - - +
1147B GLU* 1.3 58.0 + - + +
1149B PHE* 3.4 6.1 + - - +
1150B GLU* 2.9 59.9 + - + +
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Residues in contact with GLU1147 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1143B GLN* 3.2 32.0 + - - +
1144B ASN* 3.7 18.9 + - - +
1146B ILE* 1.3 77.1 - - - +
1148B GLY* 1.3 55.4 + - - +
1150B GLU* 3.5 13.7 + - - +
1151B ALA* 3.0 29.9 + - - +
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Residues in contact with GLY1148 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1127B LEU* 3.8 22.6 - - - +
1144B ASN 3.0 14.9 + - - -
1145B LEU 3.2 4.0 + - - -
1147B GLU* 1.3 75.5 - - - +
1149B PHE* 1.4 60.3 + - - +
1151B ALA* 3.4 7.6 + - - +
1152B LEU* 3.2 25.1 + - - +
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Residues in contact with PHE1149 (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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981B LEU* 4.0 34.0 - - + +
984B ALA* 4.0 11.7 - - + -
985B VAL* 3.5 26.0 - - + -
988B CYS* 4.1 2.7 - - - -
1067B PHE* 3.8 27.8 - + - -
1071B LEU* 3.8 31.0 - - + -
1124B VAL* 4.7 3.8 - - + -
1127B LEU* 3.9 20.4 - - + +
1145B LEU* 2.9 48.5 + - + +
1146B ILE* 4.0 1.3 - - - +
1148B GLY* 1.4 68.8 - - - +
1150B GLU* 1.4 60.0 + - - +
1152B LEU* 3.0 10.3 + - + +
1153B LEU* 2.9 34.2 + - + +
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Residues in contact with GLU1150 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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985B VAL* 4.7 10.0 - - + +
989B LYS* 4.2 14.2 + - - -
1146B ILE* 2.9 41.9 + - + +
1147B GLU* 3.7 13.3 - - - +
1149B PHE* 1.4 74.2 - - - +
1151B ALA* 1.4 61.4 + - - +
1153B LEU* 3.3 27.9 + - + +
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Residues in contact with ALA1151 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1147B GLU 3.0 14.3 + - - +
1148B GLY* 3.5 12.1 - - - +
1149B PHE 3.2 0.2 - - - -
1150B GLU* 1.4 75.0 - - - +
1152B LEU* 1.3 64.3 + - + +
1153B LEU 3.5 3.1 + - - -
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Residues in contact with LEU1152 (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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981B LEU* 4.3 15.7 - - + +
1123B GLU* 3.7 33.7 - - + +
1124B VAL* 3.9 26.9 - - + -
1127B LEU* 3.9 26.0 - - + -
1148B GLY 3.2 10.3 + - - +
1149B PHE* 3.0 11.7 + - + +
1151B ALA* 1.3 78.2 - - + +
1153B LEU* 1.3 62.3 + - - +
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Residues in contact with LEU1153 (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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978B LYS* 3.6 63.1 + - + +
981B LEU* 3.9 21.1 - - + +
982B LYS* 4.1 24.5 - - + -
985B VAL* 4.1 22.7 - - + -
1149B PHE 2.9 19.0 + - - +
1150B GLU* 3.3 21.4 + - + +
1151B ALA 4.5 2.7 - - - -
1152B LEU* 1.3 80.1 - - - +
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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