Contacts of the helix formed by residues 1103 - 1116 (chain A) in PDB entry 3F2B
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 ASP1103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980A GLY* 5.6 1.6 + - - -
1102A HIS* 1.3 76.3 - - - +
1104A ASP* 1.3 60.8 + - - +
1105A PRO 3.4 0.7 - - - -
1106A THR* 3.2 8.1 + - - -
1107A VAL* 2.8 30.0 + - - +
1304A VAL* 3.7 32.7 - - + +
1305A ARG* 3.7 24.8 - - - +
8T T 3.0 37.7 + - - +
9T T 4.9 7.1 + - - -
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Residues in contact with ASP1104 (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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977A ASN* 5.6 0.9 - - - +
1102A HIS* 2.9 28.6 + - + -
1103A ASP* 1.3 76.2 - - - +
1105A PRO* 1.3 65.4 - - + +
1107A VAL* 3.1 5.5 + - - +
1108A ILE* 2.9 30.2 + - - +
1156A PRO* 3.4 24.6 - - - +
1279A TYR* 5.0 9.4 - - - +
1282A MET* 3.6 32.8 - - + +
1286A ILE* 3.9 4.5 - - - +
1305A ARG* 2.8 26.8 + - - +
8T T 3.9 0.2 + - - -
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Residues in contact with PRO1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A LEU* 3.6 40.1 - - + +
891A GLY* 3.7 15.3 - - - +
977A ASN* 3.4 28.7 - - + +
978A PHE 4.5 1.3 - - - -
979A SER* 4.2 11.2 - - - +
1102A HIS* 3.6 16.4 - - + +
1103A ASP 3.6 2.5 - - - -
1104A ASP* 1.3 94.6 - - + +
1106A THR* 1.3 56.2 + - - +
1108A ILE* 3.5 0.8 + - + -
1109A ARG* 2.9 30.8 + - - +
1282A MET* 5.9 1.8 - - + -
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Residues in contact with THR1106 (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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888A TYR* 5.9 0.2 - - + -
979A SER* 2.8 29.7 + - - +
980A GLY 3.8 2.4 + - - -
981A GLU* 3.8 25.7 + - + +
1102A HIS 3.4 11.3 + - - -
1103A ASP* 3.2 8.6 + - - -
1105A PRO* 1.3 74.3 - - - +
1107A VAL* 1.3 66.8 + - - +
1109A ARG* 3.3 10.0 + - + +
1110A MET* 3.0 24.7 + - + +
1304A VAL* 3.8 26.2 - - + -
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Residues in contact with VAL1107 (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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1103A ASP 2.8 16.6 + - - +
1104A ASP* 3.6 3.1 - - - +
1106A THR* 1.3 74.4 - - - +
1108A ILE* 1.3 59.7 + - - +
1110A MET* 3.2 2.1 + - - +
1111A LEU* 2.8 47.0 + - + +
1286A ILE* 4.0 24.7 - - + -
1297A TYR* 6.0 0.4 - - + -
1300A SER* 3.7 13.6 - - - +
1301A TYR* 5.2 0.7 - - - -
1304A VAL* 3.5 33.4 - - + -
1305A ARG* 3.4 31.0 - - + +
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Residues in contact with ILE1108 (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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889A LEU* 3.8 22.7 - - + -
1104A ASP 2.9 19.6 + - - +
1105A PRO* 4.5 3.4 - - + +
1107A VAL* 1.3 77.7 - - - +
1109A ARG* 1.3 58.7 + - - +
1111A LEU* 3.6 9.6 - - + +
1112A GLN* 2.9 26.9 + - - +
1119A PRO* 2.9 40.6 - - + +
1282A MET* 4.5 13.5 - - + -
1285A ARG* 4.1 24.5 - - + +
1286A ILE* 4.1 23.3 - - + -
1289A PHE* 5.4 5.1 - - + -
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Residues in contact with ARG1109 (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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887A GLY* 3.0 30.7 + - - -
888A TYR* 3.2 51.5 + - - +
889A LEU* 3.9 17.7 - - + +
981A GLU* 4.0 7.9 + - - -
1105A PRO 2.9 20.0 + - - +
1106A THR* 3.6 10.5 - - - +
1108A ILE* 1.3 79.0 - - - +
1110A MET* 1.3 57.7 + - + +
1112A GLN* 3.3 3.6 + - - +
1113A ASP* 2.8 57.7 + - - +
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Residues in contact with MET1110 (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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1106A THR* 3.0 17.0 + - + +
1107A VAL* 3.8 3.1 - - - +
1109A ARG* 1.3 76.2 - - + +
1111A LEU* 1.3 67.7 + - - +
1113A ASP* 4.3 6.3 - - + +
1114A LEU* 3.2 43.4 + - + +
1299A ALA* 4.0 5.6 - - + -
1300A SER* 3.6 33.4 - - - +
1303A THR* 3.6 36.6 - - + +
1304A VAL* 4.2 8.7 - - + -
1371A GLU* 4.0 24.0 - - + +
1372A PHE 4.5 0.7 - - - +
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Residues in contact with LEU1111 (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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1107A VAL* 2.8 35.5 + - + +
1108A ILE* 3.6 8.5 - - - +
1109A ARG 3.3 0.2 - - - -
1110A MET* 1.3 77.4 - - - +
1112A GLN* 1.3 56.3 + - - +
1114A LEU* 3.6 3.9 + - + +
1115A SER* 3.0 30.7 + - - -
1286A ILE* 5.1 4.5 - - + -
1289A PHE* 3.5 51.9 - - + -
1296A LEU* 3.5 38.5 - - + +
1297A TYR* 3.8 10.1 - - + +
1300A SER* 2.9 26.5 - - - +
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Residues in contact with GLN1112 (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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889A LEU* 4.1 12.8 - - - +
1108A ILE 2.9 15.8 + - - +
1109A ARG* 3.7 4.2 - - - +
1110A MET 3.1 0.2 - - - -
1111A LEU* 1.3 73.3 - - - +
1113A ASP* 1.3 64.7 + - - +
1114A LEU 2.8 5.8 + - - -
1115A SER* 4.1 1.6 - - - -
1116A GLY* 2.9 31.0 + - - -
1117A ILE 3.0 20.4 - - - +
1118A ASP* 3.4 20.8 + - - +
1119A PRO* 3.3 31.3 - - + +
1289A PHE* 4.7 1.7 - - + -
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Residues in contact with ASP1113 (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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887A GLY 5.5 0.2 - - - +
1109A ARG* 2.8 61.0 + - - +
1110A MET* 3.2 8.0 + - - +
1112A GLN* 1.3 78.7 - - - +
1114A LEU* 1.3 60.7 + - + +
1116A GLY* 4.7 1.1 - - - -
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Residues in contact with LEU1114 (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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1110A MET* 3.3 43.5 - - + +
1111A LEU* 3.9 4.3 - - - +
1112A GLN 2.8 0.8 - - - -
1113A ASP* 1.3 85.6 - - + +
1115A SER* 1.3 61.0 + - - +
1116A GLY 3.6 0.4 - - - -
1296A LEU* 4.0 36.1 - - + +
1299A ALA* 4.8 1.3 - - + -
1371A GLU* 5.0 9.6 - - - +
1374A ILE* 4.4 17.5 - - + -
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Residues in contact with SER1115 (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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1111A LEU 3.0 17.6 + - - -
1112A GLN* 4.1 0.2 - - - -
1114A LEU* 1.3 76.7 - - - +
1116A GLY* 1.3 60.9 + - - +
1117A ILE* 3.1 41.0 + - - +
1289A PHE* 3.2 13.6 - - - -
1293A HIS* 5.2 4.5 - - - -
1296A LEU* 3.7 17.0 - - - -
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Residues in contact with GLY1116 (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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1112A GLN* 2.9 18.2 + - - -
1113A ASP 4.7 0.8 - - - -
1114A LEU 3.6 1.4 - - - +
1115A SER* 1.3 78.2 - - - +
1117A ILE* 1.3 62.4 + - - +
1118A ASP* 3.7 2.1 + - - +
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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