Contacts of the helix formed by residues 1056 - 1063 (chain A) in PDB entry 6S1M
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 THR1056 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1052A SER 3.3 20.6 + - - +
1053A ARG* 4.1 5.4 - - - +
1055A TRP* 1.3 76.0 - - - +
1057A GLN* 1.3 64.8 + - - +
1058A CYS 3.3 1.6 - - - -
1059A GLN* 3.4 31.4 + - - +
1060A ARG* 3.4 30.1 + - - +
50B TYR* 4.2 13.2 - - - -
379B PRO* 3.8 16.4 + - - -
380B ASP* 4.0 22.2 + - - +
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Residues in contact with GLN1057 (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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1053A ARG 3.6 13.0 - - - +
1054A LEU 3.2 10.4 + - - +
1056A THR* 1.3 79.3 - - - +
1058A CYS* 1.3 59.2 + - - +
1059A GLN 3.2 0.2 - - - -
1060A ARG* 3.2 25.7 + - - +
1061A CYS* 3.0 35.4 + - - +
1078A ILE* 4.1 16.6 - - + -
1202A SF4 4.1 6.9 - - - -
106B SER* 2.5 29.6 + - - -
107B ILE* 3.8 18.0 + - + +
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Residues in contact with CYS1058 (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 LEU 3.6 7.7 + - - +
1055A TRP* 4.5 12.1 - - + +
1056A THR 3.3 0.4 - - - -
1057A GLN* 1.3 80.0 - - - +
1059A GLN* 1.3 55.3 + - - +
1061A CYS* 3.8 0.7 - - - +
1062A GLN* 2.9 32.4 + - - +
1069A VAL* 3.8 24.4 - - + +
1078A ILE* 3.4 13.2 - - - -
1082A ARG* 3.5 26.0 - - - -
1202A SF4 2.3 42.5 - - - -
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Residues in contact with GLN1059 (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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1055A TRP 4.5 8.5 - - - +
1056A THR* 3.4 25.9 + - - +
1057A GLN 3.2 0.4 - - - -
1058A CYS* 1.3 80.0 - - - +
1060A ARG* 1.3 57.1 + - - +
1062A GLN* 4.1 4.4 - - - +
1063A GLY 3.3 16.1 + - - -
1064A SER 3.1 28.9 + - - +
1065A LEU* 3.7 39.4 + - + +
1067A GLU 5.2 2.6 + - - +
1069A VAL* 4.6 12.3 - - + -
50B TYR* 3.5 40.3 + - - +
51B ALA* 3.7 8.9 - - - +
54B TYR* 4.0 10.7 + - - -
379B PRO 5.0 0.2 - - - +
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Residues in contact with ARG1060 (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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1053A ARG* 4.4 3.6 + - - +
1056A THR* 3.4 36.5 + - - +
1057A GLN* 3.2 36.6 + - - +
1059A GLN* 1.3 78.7 - - - +
1061A CYS* 1.3 60.8 + - - +
1062A GLN 3.3 0.4 - - - -
1063A GLY* 3.9 8.1 + - - +
1065A LEU* 5.3 4.0 - - + -
98B PHE* 4.4 27.6 - - + -
104B GLN* 4.2 22.9 + - - +
105B PRO 4.7 8.9 + - - -
106B SER* 4.5 8.7 + - - +
107B ILE* 6.0 1.0 - - - +
380B ASP* 4.3 22.4 + - - +
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Residues in contact with CYS1061 (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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484A GLU* 4.6 25.9 - - - +
1057A GLN* 3.0 28.6 + - - +
1058A CYS 4.1 2.9 - - - +
1060A ARG* 1.3 75.7 - - - +
1062A GLN* 1.3 61.1 + - - +
1202A SF4 2.4 43.3 - - - -
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Residues in contact with GLN1062 (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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507A ARG* 3.2 18.2 - - - +
1058A CYS 2.9 17.9 + - - +
1059A GLN* 4.1 4.7 - - - +
1061A CYS* 1.3 79.1 - - - +
1063A GLY* 1.3 56.0 + - - +
1064A SER* 3.0 36.1 + - - +
1067A GLU 3.7 8.0 + - - +
1068A ASP 2.4 37.6 + - - -
1069A VAL* 3.5 17.3 - - + +
1070A ILE 4.5 1.3 - - - +
1202A SF4 5.3 3.4 - - - -
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Residues in contact with GLY1063 (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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1059A GLN 3.3 9.4 + - - -
1060A ARG* 3.9 7.4 + - - -
1061A CYS 3.5 2.0 - - - -
1062A GLN* 1.3 78.8 - - - +
1064A SER* 1.3 57.7 + - - +
1065A LEU* 5.5 1.4 - - - +
136B GLU* 4.2 2.8 - - - +
141B ARG* 3.8 30.0 + - - -
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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