Contacts of the helix formed by residues 1116 - 1126 (chain H) in PDB entry 6C3P
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 PRO1116 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824H GLU 3.3 24.2 - - - +
825H ARG* 3.8 18.8 - - - +
826H GLY 4.5 6.5 - - - +
1114H THR 3.7 6.5 - - - +
1115H THR* 1.3 103.2 - - + +
1117H LEU* 1.3 65.1 + - - +
1118H GLY 3.4 1.6 + - - +
1119H SER* 3.4 19.3 + - - +
1120H ILE* 3.7 2.8 + - - -
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Residues in contact with LEU1117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503H LEU* 3.5 40.1 - - + +
504H ARG* 4.4 29.4 - - - +
506H ILE* 5.2 2.0 - - + -
824H GLU 4.5 2.8 + - - -
1112H PHE* 4.7 26.0 - - + +
1115H THR 3.7 1.5 + - - +
1116H PRO* 1.3 72.6 - - - +
1118H GLY* 1.3 67.0 + - - +
1119H SER 3.2 0.2 + - - -
1120H ILE* 3.3 13.2 - - + +
1121H LEU* 2.9 28.0 + - + +
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Residues in contact with GLY1118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824H GLU* 4.8 7.3 + - - +
1116H PRO* 3.3 2.8 - - - +
1117H LEU* 1.3 78.0 - - - +
1119H SER* 1.3 61.0 + - - +
1121H LEU* 3.6 11.2 - - - +
1122H ASN* 2.9 25.3 + - - +
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Residues in contact with SER1119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115H THR* 4.9 7.0 - - - -
1116H PRO* 3.4 19.7 + - - +
1117H LEU 3.2 0.6 - - - -
1118H GLY* 1.3 74.6 - - - +
1120H ILE* 1.3 55.8 + - - +
1122H ASN* 2.8 27.6 + - - +
1123H ARG* 3.0 31.5 - - - +
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Residues in contact with ILE1120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503H LEU* 4.7 10.5 - - + +
1100H LEU* 6.0 0.7 - - + -
1104H ILE* 3.7 41.7 - - + -
1111H PHE* 3.9 26.7 - - + -
1112H PHE* 5.8 4.5 - - + -
1115H THR* 4.3 14.5 - - + +
1116H PRO 3.7 10.0 + - - +
1117H LEU* 3.3 25.4 - - + +
1119H SER* 1.3 77.7 - - - +
1121H LEU* 1.3 63.5 + - - +
1123H ARG* 3.8 11.8 + - + +
1124H PHE* 3.7 16.7 - - + -
1317H LEU* 4.2 22.4 - - + -
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Residues in contact with LEU1121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496H LEU* 6.0 0.2 - - + -
499H THR* 3.9 29.8 - - + +
500H ASN* 3.1 34.1 - - - +
503H LEU* 4.9 9.9 - - + -
504H ARG* 3.9 24.5 - - - +
1117H LEU* 2.9 20.5 + - + +
1118H GLY* 3.6 9.9 - - - +
1120H ILE* 1.3 76.2 - - + +
1122H ASN* 1.3 66.7 + - - +
1123H ARG 3.1 2.9 + - - -
1124H PHE* 3.1 8.4 + - + +
1125H SER* 2.9 24.5 + - - -
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Residues in contact with ASN1122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118H GLY 2.9 13.2 + - - +
1119H SER* 2.8 17.0 + - - +
1121H LEU* 1.3 73.2 - - - +
1123H ARG* 1.3 72.4 + - - +
1125H SER* 3.8 9.5 + - - -
1126H SER* 2.8 43.0 + - - -
1127H ASP* 3.1 10.5 + - - -
1197H LEU* 5.2 12.7 - - - +
1200H LEU* 5.2 11.2 - - - +
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Residues in contact with ARG1123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100H LEU* 4.5 11.6 - - + +
1119H SER* 3.0 43.7 + - - +
1120H ILE* 4.0 9.6 - - + +
1121H LEU 3.1 1.0 - - - -
1122H ASN* 1.3 93.6 - - - +
1124H PHE* 1.3 58.8 + - + +
1127H ASP* 3.2 33.7 + - - +
1128H CYS* 2.9 26.5 + - - +
1313H ARG* 3.3 28.6 - - + +
1314H ILE* 3.6 22.1 - - + +
1317H LEU* 3.2 34.7 - - + +
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Residues in contact with PHE1124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495H ARG* 2.8 35.6 + - - +
499H THR* 4.6 19.5 - - + +
503H LEU* 5.4 4.5 - - + -
1097H HIS* 4.1 24.2 - + - -
1100H LEU* 3.5 34.5 - - + -
1101H LEU* 3.6 47.1 - - + -
1104H ILE* 3.8 26.2 - - + -
1120H ILE* 3.7 19.3 - - + -
1121H LEU* 3.1 7.4 + - - +
1123H ARG* 1.3 79.4 - - + +
1125H SER* 1.3 63.6 + - - +
1128H CYS* 3.7 13.2 - - + +
1129H ASN 4.4 0.2 + - - -
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Residues in contact with SER1125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419H ASN* 5.2 7.4 + - - -
423H ILE* 6.0 0.3 - - - +
492H SER* 5.7 0.2 + - - -
495H ARG* 4.2 2.3 + - - -
496H LEU* 3.5 33.4 - - - +
500H ASN* 5.7 0.7 - - - -
1121H LEU* 2.9 25.7 + - - +
1122H ASN* 3.1 13.5 + - - -
1124H PHE* 1.3 81.4 - - - +
1126H SER* 1.3 60.8 + - - +
1129H ASN* 3.6 16.5 + - - +
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Residues in contact with SER1126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423H ILE* 4.3 19.6 - - - +
1122H ASN* 2.8 24.6 + - - -
1125H SER* 1.3 75.6 - - - +
1127H ASP* 1.3 64.2 + - - +
1128H CYS 3.5 1.3 - - - -
1129H ASN* 3.4 8.3 - - - +
1130H THR* 2.8 38.5 + - - -
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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