Contacts of the helix formed by residues 1152 - 1161 (chain A) in PDB entry 6CNC
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 ARG1152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1149A ASN* 5.2 4.3 - - + +
1150A ASP 3.9 0.2 + - - -
1151A GLU* 1.3 90.7 - - + +
1153A ALA* 1.3 62.0 + - + +
1155A ARG* 2.7 9.2 + - - +
1156A VAL* 2.3 42.1 + - + -
1197A GLN* 3.2 25.4 + - - +
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Residues in contact with ALA1153 (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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1145A LEU* 4.7 9.0 - - + -
1147A ASN* 4.0 23.3 - - - +
1149A ASN* 4.3 13.9 - - + +
1151A GLU 3.1 3.4 + - - -
1152A ARG* 1.3 77.3 - - + +
1154A ALA* 1.3 56.4 + - - +
1156A VAL* 3.7 9.0 - - - -
1157A VAL* 2.8 38.1 + - + +
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Residues in contact with ALA1154 (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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1145A LEU* 4.4 8.2 - - + +
1149A ASN 3.1 21.9 + - - +
1150A ASP* 3.4 9.2 - - - +
1152A ARG 2.8 2.6 + - - -
1153A ALA* 1.3 77.8 - - - +
1155A ARG* 1.3 53.3 + - + +
1157A VAL* 3.1 8.7 - - - +
1158A LYS* 2.5 37.5 + - - +
1283A ILE* 3.5 28.7 - - + -
1293A LEU* 5.0 1.6 - - - +
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Residues in contact with ARG1155 (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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1150A ASP* 3.3 19.8 + - - +
1151A GLU* 3.9 19.1 + - - -
1152A ARG 2.7 13.0 + - - +
1154A ALA* 1.3 77.2 - - + +
1156A VAL* 1.3 61.1 + - - +
1158A LYS* 3.6 31.2 - - + +
1159A GLY* 2.9 17.3 + - - -
1195A LYS 5.5 6.4 + - - -
1196A LEU* 5.3 10.5 - - - +
1197A GLN* 3.5 22.9 + - + +
1283A ILE* 5.5 12.1 - - + +
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Residues in contact with VAL1156 (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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1152A ARG* 2.3 51.1 + - + +
1153A ALA* 3.4 10.8 - - - +
1155A ARG* 1.3 70.2 - - - +
1157A VAL* 1.3 60.0 + - + +
1159A GLY* 3.1 1.6 + - - -
1160A ARG* 2.9 49.2 + - - +
1197A GLN* 4.0 21.5 - - + +
1199A GLU* 3.3 28.0 - - - +
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Residues in contact with VAL1157 (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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1145A LEU* 2.5 39.9 - - + -
1153A ALA* 2.8 18.8 + - - +
1154A ALA 3.1 10.3 - - - +
1156A VAL* 1.3 70.5 - - + +
1158A LYS* 1.3 66.7 + - - +
1160A ARG* 3.0 32.7 + - + +
1161A VAL* 3.3 12.0 + - - +
1293A LEU* 3.7 10.0 - - + +
1306A THR* 5.5 2.0 - - + +
1307A ASP 3.7 8.7 - - - +
1308A GLY* 3.6 31.2 - - - -
1309A VAL* 4.5 4.3 - - + -
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Residues in contact with LYS1158 (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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1154A ALA 2.5 23.0 + - - +
1155A ARG* 3.6 31.8 - - + +
1157A VAL* 1.3 73.8 - - - +
1159A GLY* 1.3 56.3 + - - +
1161A VAL 2.8 27.7 - - - +
1162A GLU* 3.9 21.5 + - - +
1196A LEU* 5.3 9.5 - - - +
1281A ALA* 3.4 32.4 + - + +
1282A VAL* 4.6 2.0 - - - +
1283A ILE* 4.4 32.3 - - + +
1293A LEU* 4.7 11.7 - - + -
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Residues in contact with GLY1159 (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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1155A ARG 2.9 15.2 + - - -
1156A VAL 3.6 3.8 - - - -
1158A LYS* 1.3 73.3 - - - +
1160A ARG* 1.3 65.7 + - - +
1161A VAL 3.1 3.8 + - - -
1162A GLU* 3.8 14.6 + - - +
1165A LEU* 5.0 2.6 - - - +
1197A GLN 4.2 9.2 - - - -
1198A LEU* 4.1 27.7 - - - +
1199A GLU* 5.4 0.7 - - - -
1273A LYS* 4.6 8.2 - - - +
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Residues in contact with ARG1160 (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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1156A VAL* 2.9 31.9 + - - +
1157A VAL* 3.0 26.1 + - - +
1159A GLY* 1.3 76.3 - - - +
1161A VAL* 1.3 65.4 + - - +
1199A GLU* 3.2 35.1 + - - +
1273A LYS* 4.3 17.4 + - - +
1274A GLY* 4.1 10.9 + - - -
1275A LEU* 4.6 2.8 - - - +
1306A THR* 4.3 14.0 - - + +
1307A ASP* 2.3 54.6 + - - +
1308A GLY* 3.7 2.6 - - - +
7E ARG* 4.4 17.1 - - - +
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Residues in contact with VAL1161 (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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1157A VAL 3.3 7.1 + - - +
1158A LYS 2.8 18.4 - - - +
1160A ARG* 1.3 83.4 - - - +
1162A GLU* 1.3 62.7 + - - +
1274A GLY* 4.3 2.9 - - - -
1275A LEU* 3.5 38.6 - - + +
1278A ILE* 3.5 36.3 - - + -
1281A ALA* 3.7 13.9 - - - +
1295A VAL* 5.7 3.4 - - + -
1303A VAL* 5.1 7.2 - - + -
1306A THR* 3.7 27.1 - - + +
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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