Contacts of the helix formed by residues 1055 - 1060 (chain A) in PDB entry 3M5M
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 VAL1055 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043A PHE* 4.4 2.9 - - + -
1054A THR* 1.3 91.8 + - - +
1056A TYR* 1.3 65.2 + - - +
1057A HIS* 3.7 22.7 - - + +
1058A GLY* 3.2 16.4 + - - +
1059A ALA* 3.0 24.3 + - - +
1081A ASP* 3.2 18.2 - - - +
1083A VAL* 4.5 1.1 - - - -
1139A ALA* 3.6 28.5 - - + +
1140A GLY* 3.9 4.5 - - - +
1153A ILE* 4.7 0.7 - - + -
1154A PHE 3.8 22.2 - - - +
1155A ARG* 4.2 5.6 - - - -
1170A ILE* 4.6 6.5 - - + -
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Residues in contact with TYR1056 (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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1054A THR 3.9 0.2 + - - -
1055A VAL* 1.3 71.0 - - - +
1057A HIS* 1.3 62.8 + - - +
1060A GLY* 2.7 58.8 + - - +
1061A THR* 3.7 22.0 + - + +
1076A THR* 3.9 13.2 - - + -
1078A VAL* 3.7 40.4 - - + -
1081A ASP* 3.0 19.0 + - - +
1082A LEU 3.8 13.6 - - - +
1083A VAL* 3.6 18.0 - - + +
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Residues in contact with HIS1057 (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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2A SO4 3.9 7.0 + - - -
1041A GLN* 3.0 26.1 + - - -
1055A VAL* 3.2 7.9 - - + +
1056A TYR* 1.3 77.0 - - + +
1058A GLY* 1.3 59.8 + - - +
1081A ASP* 2.6 38.5 + - - +
1139A ALA* 3.5 16.0 - - + +
1155A ARG 3.3 26.7 - - - -
1156A ALA* 5.5 1.1 - - + -
1183A SO4 2.7 28.0 + - - -
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Residues in contact with GLY1058 (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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2A SO4 4.6 1.4 + - - -
1038A THR* 4.0 4.7 - - - +
1041A GLN* 3.7 21.8 + - - -
1043A PHE* 3.3 29.3 - - - -
1055A VAL* 3.2 10.9 + - - +
1056A TYR 3.0 0.6 - - - -
1057A HIS* 1.3 84.9 - - - +
1059A ALA* 1.3 61.7 + - - +
1060A GLY 3.5 0.7 - - - -
1062A ARG* 3.5 11.6 + - - -
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Residues in contact with ALA1059 (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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992A VAL* 4.0 11.9 - - + -
1043A PHE* 3.5 6.3 - - + -
1054A THR* 3.7 21.1 - - + -
1055A VAL 3.0 13.3 + - - +
1058A GLY* 1.3 73.7 - - - +
1060A GLY* 1.3 68.4 - - - +
1062A ARG* 3.1 35.0 + - - +
1083A VAL* 4.0 3.6 - - + -
1085A TRP* 3.9 18.8 - - + -
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Residues in contact with GLY1060 (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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1056A TYR* 2.7 47.7 + - - -
1058A GLY 3.5 1.6 + - - -
1059A ALA* 1.3 71.4 - - - +
1061A THR* 1.3 51.5 + - - -
1062A ARG* 3.9 5.8 - - - +
1073A GLN* 2.8 22.5 + - - -
1083A VAL* 3.5 15.4 - - - +
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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