Contacts of the helix formed by residues 1085 - 1093 (chain B) in PDB entry 5M64
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 SER1085 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1646A LEU* 3.8 10.4 - - - +
1647A ASN* 2.8 41.0 + - - +
1649A VAL 3.3 23.3 - - - -
1651A THR* 3.6 10.7 - - - +
1652A GLY* 3.3 21.8 - - - -
1080B ILE* 4.9 0.7 - - - -
1083B GLY 3.5 1.4 + - - -
1084B THR* 1.3 72.5 + - - +
1086B PHE* 1.3 66.6 + - - +
1087B LEU 3.2 1.6 - - - -
1088B LEU* 3.2 13.9 - - - +
1089B GLN* 3.7 3.3 + - - +
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Residues in contact with PHE1086 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 5.8 1.6 - - + -
640A ASN* 3.3 46.9 - - + -
642A ASN* 3.1 39.5 - - + +
643A ALA* 3.9 11.4 - - + -
646A GLU* 5.4 4.3 - - + -
1646A LEU* 3.7 27.8 - - + -
1651A THR* 3.9 10.6 - - + +
1084B THR* 3.9 1.7 + - - +
1085B SER* 1.3 78.2 + - - +
1087B LEU* 1.3 65.0 + - - +
1089B GLN* 3.2 14.4 + - + +
1090B ASP* 3.0 22.7 + - + +
92F ARG* 5.9 0.4 - - - +
99F LEU* 6.1 3.1 - - + -
109G PRO 3.9 18.4 - - - -
110G ASP* 4.9 15.9 - - - -
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Residues in contact with LEU1087 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A LEU* 5.0 14.8 - - + -
600A MET* 4.6 10.5 - - + -
638A PRO* 5.2 5.4 - - + -
643A ALA* 4.1 14.6 - - + +
646A GLU* 3.2 31.9 + - - +
647A ALA* 5.6 2.5 - - + -
651A ALA* 5.3 6.7 - - + -
1079B LEU* 3.6 24.0 - - + -
1084B THR* 3.2 27.9 + - + +
1085B SER 3.2 1.2 - - - -
1086B PHE* 1.3 79.3 - - - +
1088B LEU* 1.3 50.2 + - - +
1090B ASP* 3.2 8.6 + - - +
1091B ARG* 2.5 46.0 + - + +
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Residues in contact with LEU1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1637A PRO* 6.1 0.2 - - + -
1640A ARG 4.9 2.9 - - - +
1641A ILE* 3.7 22.6 - - + +
1646A LEU 3.7 11.2 - - - +
1647A ASN* 3.1 42.2 - - - +
1076B ARG* 3.2 41.1 - - - +
1079B LEU* 3.6 16.6 - - + +
1080B ILE* 3.7 17.3 - - + -
1084B THR 4.4 3.2 + - - +
1085B SER 3.2 4.0 + - - +
1087B LEU* 1.3 75.2 - - - +
1089B GLN* 1.3 67.1 + - - +
1091B ARG* 3.9 0.9 - - - -
1092B LEU* 2.8 34.6 + - + +
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Residues in contact with GLN1089 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 5.5 5.6 - - + +
1640A ARG 5.0 1.4 - - - +
1641A ILE* 6.0 0.9 - - - +
1643A VAL 5.6 1.4 + - - -
1644A GLY* 4.7 13.9 + - - -
1645A LYS 3.8 20.5 + - - +
1646A LEU* 4.1 33.4 - - + +
1085B SER 3.7 3.5 + - - +
1086B PHE* 3.2 19.3 + - + +
1088B LEU* 1.3 86.2 - - + +
1090B ASP* 1.3 57.6 + - - +
1093B LEU* 3.2 45.4 + - + +
1094B ASN* 3.1 22.3 + - - +
110G ASP* 4.8 13.2 + - - +
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Residues in contact with ASP1090 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A VAL* 5.7 0.3 - - - +
637A PHE 4.9 1.2 - - - +
638A PRO* 3.8 10.2 - - - +
639A GLN* 3.5 33.6 + - - +
640A ASN* 2.8 32.6 + - - +
643A ALA* 4.4 7.5 - - + +
1086B PHE* 3.0 18.1 + - + +
1087B LEU* 3.7 8.6 - - - +
1089B GLN* 1.3 77.5 - - - +
1091B ARG* 1.3 63.7 + - - +
1092B LEU 3.4 1.1 + - - -
1094B ASN* 3.4 27.4 + - - +
1095B SER* 3.8 7.8 + - - -
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Residues in contact with ARG1091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A VAL* 3.3 60.4 - - - +
588A LEU* 4.5 8.2 - - - +
600A MET* 4.7 0.8 - - - +
636A HIS* 3.0 56.8 + - - +
1069B ILE* 5.4 0.6 - - - +
1071B VAL* 3.3 33.3 - - + +
1075B GLU* 3.8 21.8 + - - +
1079B LEU* 3.8 29.8 - - + -
1087B LEU* 2.5 29.5 + - + +
1088B LEU* 3.9 0.4 - - - -
1090B ASP* 1.3 77.0 + - - +
1092B LEU* 1.3 57.5 + - + +
1095B SER* 3.9 2.3 + - - -
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Residues in contact with LEU1092 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A MET 5.4 0.4 - - - +
472A MET 3.7 13.5 - - - +
473A GLY* 3.8 2.7 - - - -
474A LYS* 3.4 69.7 + - + +
476A VAL* 5.2 0.7 - - + -
1641A ILE* 3.8 42.2 - - + +
1071B VAL* 5.2 8.3 - - + -
1076B ARG* 5.4 4.7 - - - -
1079B LEU* 5.9 1.3 - - + -
1088B LEU* 2.8 20.5 + - + +
1091B ARG* 1.3 82.4 - - + +
1093B LEU* 1.3 62.1 + - + +
1095B SER* 3.7 11.4 + - - -
1097B ASP* 4.4 2.4 - - - +
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Residues in contact with LEU1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.8 7.2 - - + -
474A LYS* 5.1 2.2 - - - +
1643A VAL 5.6 5.2 - - - +
1089B GLN* 3.2 42.0 + - - +
1092B LEU* 1.3 80.7 - - + +
1094B ASN* 1.3 65.0 + - - +
1095B SER 3.2 6.3 + - - -
1097B ASP* 3.3 30.1 + - + +
1098B TYR* 3.6 46.0 + - + +
1177B ALA* 5.6 4.7 - - + -
1178B ILE 5.3 1.1 - - - +
1179B PRO* 4.1 22.9 - - + -
110G ASP* 5.9 0.2 - - - +
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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