Contacts of the helix formed by residues 1154 - 1163 (chain A) in PDB entry 4DDG
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 SER1154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105A LEU* 4.7 0.4 - - - +
1152A GLN* 3.4 13.3 - - - +
1153A THR* 1.3 81.7 + - - +
1155A VAL* 1.3 68.3 + - - +
1156A ALA* 2.9 15.6 + - - +
1157A ASP* 3.0 26.9 + - - +
1158A LEU 3.9 0.7 + - - -
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Residues in contact with VAL1155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051A ARG* 4.8 13.9 - - - +
1083A ARG* 5.0 6.1 - - - +
1098A PHE* 5.3 1.3 - - + -
1102A GLU* 3.3 42.0 - - + +
1105A LEU* 3.6 21.0 - - + +
1153A THR 3.6 0.8 + - - -
1154A SER* 1.3 73.4 - - - +
1156A ALA* 1.3 61.9 + - + +
1157A ASP 3.3 0.2 + - - -
1158A LEU* 3.3 14.2 - - + +
1159A LEU* 2.9 30.6 + - - +
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Residues in contact with ALA1156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154A SER* 2.9 10.9 + - - +
1155A VAL* 1.3 85.2 - - + +
1157A ASP* 1.3 58.5 + - - +
1159A LEU* 3.5 17.2 - - + +
1160A ALA* 2.9 26.5 + - - +
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Residues in contact with ASP1157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148A GLN* 4.5 2.5 - - - +
1153A THR* 3.0 31.9 + - + +
1154A SER* 3.0 12.1 + - - +
1156A ALA* 1.3 76.0 - - - +
1158A LEU* 1.3 60.8 + - - +
1159A LEU 3.2 0.9 - - - -
1160A ALA* 3.1 11.5 + - - +
1161A SER* 2.9 27.3 + - - -
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Residues in contact with LEU1158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098A PHE* 3.6 23.6 - - + -
1101A LEU* 3.9 32.5 - - + -
1102A GLU* 4.5 10.8 - - + +
1105A LEU* 4.2 12.8 - - + -
1145A LEU* 4.9 7.2 - - + +
1148A GLN* 3.8 20.6 + - + +
1149A VAL* 4.9 7.6 - - + -
1153A THR* 4.4 11.3 - - + +
1154A SER 3.9 2.0 + - - -
1155A VAL* 3.3 31.5 + - - +
1157A ASP* 1.3 75.2 - - - +
1159A LEU* 1.3 59.1 + - - +
1161A SER* 3.1 4.7 + - - -
1162A PHE* 2.9 47.8 + - + -
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Residues in contact with LEU1159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048A VAL* 3.9 19.1 - - + +
1049A SER 3.7 15.0 - - - +
1050A GLU* 4.5 8.7 - - + -
1083A ARG* 3.3 28.3 - - - +
1098A PHE* 3.6 15.9 - - + -
1155A VAL 2.9 20.5 + - - +
1156A ALA* 3.5 16.2 - - + +
1157A ASP 3.2 0.2 - - - -
1158A LEU* 1.3 75.3 - - - +
1160A ALA* 1.3 69.6 + - + +
1162A PHE* 3.0 12.3 + - - +
1163A ASN* 3.0 31.1 + - - +
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Residues in contact with ALA1160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156A ALA 2.9 17.1 + - - +
1157A ASP* 3.1 17.0 + - - +
1159A LEU* 1.3 80.3 - - + +
1161A SER* 1.3 61.2 + - - +
1163A ASN* 3.5 13.3 + - - +
1164A ASP* 3.6 9.7 + - - +
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Residues in contact with SER1161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145A LEU* 4.1 12.8 - - - -
1148A GLN* 2.5 41.9 + - - -
1157A ASP 2.9 10.0 + - - -
1158A LEU* 3.3 9.4 - - - -
1159A LEU 3.1 0.2 - - - -
1160A ALA* 1.3 77.0 - - - +
1162A PHE* 1.3 62.8 + - - +
1164A ASP* 3.2 23.2 + - - +
1167A THR* 3.9 14.8 - - - +
1168A SER 4.4 0.2 + - - -
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Residues in contact with PHE1162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047A LEU* 3.8 11.3 - - - +
1048A VAL* 4.1 15.5 - - + +
1094A ARG* 4.0 8.3 - - + -
1097A GLY 4.0 3.1 - - - -
1098A PHE* 3.4 57.2 - + + -
1101A LEU* 4.1 9.2 - - + -
1145A LEU* 4.5 11.7 - - + -
1158A LEU* 2.9 38.9 + - + +
1159A LEU* 3.0 8.0 + - - +
1161A SER* 1.3 78.9 - - - +
1163A ASN* 1.3 58.5 + - - +
1164A ASP 3.3 0.4 - - - -
1168A SER* 3.2 39.9 + - - +
1171A LEU* 3.6 39.9 - - + -
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Residues in contact with ASN1163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046A PRO* 3.9 6.8 - - - +
1047A LEU* 3.4 26.7 + - + +
1048A VAL* 3.0 46.4 + - - +
1159A LEU* 3.0 40.4 + - - +
1160A ALA* 4.1 7.8 - - - +
1161A SER 3.2 0.8 - - - -
1162A PHE* 1.3 75.1 - - - +
1164A ASP* 1.3 63.0 + - - +
1165A GLN 3.7 0.9 + - - -
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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