Contacts of the helix formed by residues 1254 - 1267 (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 ASN1254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1253A GLU* 1.3 91.4 + - - +
1255A ASP* 1.3 62.2 + - - +
1256A VAL* 3.1 5.8 - - - +
1257A PHE* 3.1 18.2 + - + +
1258A TYR* 3.7 13.1 + - + -
13I LEU* 3.6 22.4 - - + +
14I ILE 4.1 7.2 - - - +
15I THR* 2.8 34.5 + - - -
16I SER* 2.9 26.9 + - - +
27I ARG* 5.4 11.1 - - - +
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Residues in contact with ASP1255 (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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1236A PRO* 5.5 11.0 - - + +
1252A SER 4.2 13.9 - - - +
1253A GLU* 3.0 4.1 - - - +
1254A ASN* 1.3 75.5 - - - +
1256A VAL* 1.3 66.6 + - + +
1257A PHE 3.1 0.7 - - - -
1258A TYR* 3.1 18.2 + - - +
1259A ARG* 2.9 48.0 + - - +
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Residues in contact with VAL1256 (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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1182A SER* 5.5 0.4 - - - +
1234A VAL* 4.6 19.5 - - + +
1235A PHE* 4.1 7.2 - - - -
1236A PRO* 3.6 40.4 - - + -
1254A ASN* 4.9 2.9 - - - -
1255A ASP* 1.3 79.8 + - - +
1257A PHE* 1.3 56.6 + - - +
1259A ARG* 4.0 7.7 - - - +
1260A MET* 2.9 35.3 + - + +
14I ILE* 5.8 8.3 - - + +
16I SER* 5.3 13.5 - - - +
22I TYR* 4.6 24.2 - - + +
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Residues in contact with PHE1257 (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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1177A TYR* 5.2 0.9 - - - -
1254A ASN* 3.1 9.6 + - + +
1255A ASP 3.1 0.8 - - - -
1256A VAL* 1.3 78.3 - - - +
1258A TYR* 1.3 71.6 + + - +
1260A MET* 3.2 11.9 - - + +
1261A GLN* 2.9 36.2 + - + +
288B GLU* 3.0 37.0 - - - -
1I MET 4.3 17.5 - - - -
2I LEU 5.8 1.1 - - - -
11I MET* 5.1 2.0 - - + -
12I LEU 4.2 6.5 - - - -
13I LEU* 3.6 27.1 - - + -
14I ILE* 3.1 61.8 + - + +
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Residues in contact with TYR1258 (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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1253A GLU 5.3 4.0 - - - -
1254A ASN* 3.7 16.2 + - + -
1255A ASP* 3.1 18.2 + - - +
1257A PHE* 1.3 86.2 - + - +
1259A ARG* 1.3 66.8 + - - +
1261A GLN* 3.1 14.1 + - + +
1262A GLN* 3.1 20.7 + - + +
288B GLU* 3.2 35.0 - - + -
289B GLU* 5.4 3.8 - - + -
291B SER* 3.9 8.5 - - - -
292B LYS* 3.2 51.3 + - + -
13I LEU* 4.7 10.0 - - + +
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Residues in contact with ARG1259 (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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1216A LYS 5.5 4.4 + - - -
1217A ILE* 5.6 4.6 - - - +
1218A GLN* 5.4 10.5 - - - +
1234A VAL* 4.5 17.3 - - + -
1235A PHE 4.5 13.6 + - - +
1236A PRO* 5.7 4.2 - - - +
1255A ASP* 2.9 35.2 + - - +
1256A VAL* 4.0 6.8 - - - +
1258A TYR* 1.3 75.5 - - - +
1260A MET* 1.3 66.3 + - - +
1261A GLN 3.2 0.2 + - - -
1262A GLN* 3.3 8.8 + - - +
1263A LEU* 2.9 49.2 + - + +
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Residues in contact with MET1260 (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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1175A ASP* 3.9 11.0 - - - +
1177A TYR* 3.0 36.3 - - + +
1182A SER* 3.1 28.3 - - - +
1184A ILE* 3.4 26.0 - - + -
1234A VAL* 3.7 16.8 - - + +
1256A VAL* 2.9 26.6 + - + +
1257A PHE* 3.2 14.8 - - + +
1259A ARG* 1.3 75.6 - - - +
1261A GLN* 1.3 57.1 + - - +
1263A LEU* 3.3 10.8 + - - +
1264A ARG* 2.9 29.9 + - + +
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Residues in contact with GLN1261 (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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1257A PHE* 2.9 24.1 + - + +
1258A TYR* 3.1 13.2 + - + +
1260A MET* 1.3 76.1 - - - +
1262A GLN* 1.3 59.8 + - + +
1264A ARG* 2.8 50.7 + - - +
1265A ARG* 2.9 53.0 + - - +
284B ALA* 6.2 1.0 - - - +
288B GLU* 4.2 28.9 - - + +
1I MET 5.5 3.3 + - - -
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Residues in contact with GLN1262 (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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1216A LYS* 4.8 22.6 + - - +
1258A TYR* 3.1 12.5 + - - +
1259A ARG* 3.9 10.4 - - - +
1261A GLN* 1.3 78.1 - - + +
1263A LEU* 1.3 60.9 + - + +
1265A ARG* 3.8 16.6 - - - +
1266A ALA* 2.9 35.1 + - + +
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Residues in contact with LEU1263 (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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1184A ILE* 5.8 8.5 - - + -
1216A LYS* 5.9 4.3 - - + -
1217A ILE* 3.6 39.7 - - + -
1232A ILE* 5.1 7.6 - - + -
1234A VAL* 3.7 31.6 - - + -
1259A ARG* 2.9 40.5 + - + +
1260A MET* 3.6 12.3 - - - +
1262A GLN* 1.3 79.1 - - + +
1264A ARG* 1.3 59.8 + - - +
1265A ARG 3.2 0.9 + - - -
1267A LEU* 3.0 40.5 + - + +
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Residues in contact with ARG1264 (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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1173A VAL* 4.9 14.5 - - + +
1175A ASP* 3.7 24.7 + - - +
1184A ILE* 6.3 1.6 - - - -
1260A MET* 2.9 15.0 + - + +
1261A GLN* 2.8 35.8 + - - +
1263A LEU* 1.3 71.6 - - - +
1265A ARG* 1.3 58.6 + - - +
1267A LEU* 6.0 0.2 - - - -
1268A PRO* 3.6 15.3 - - - +
281B ASP* 5.2 12.9 - - - +
1I MET* 5.8 12.3 + - - +
2I LEU* 6.3 3.3 - - - +
39I GLU* 5.8 0.2 + - - -
41I TYR* 3.4 38.4 + - + +
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Residues in contact with ARG1265 (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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1261A GLN* 2.9 51.9 + - - +
1262A GLN* 3.6 21.4 - - - +
1263A LEU 3.1 0.2 - - - -
1264A ARG* 1.3 77.4 - - - +
1266A ALA* 1.3 65.2 + - + +
1267A LEU 3.4 0.2 - - - -
1268A PRO* 3.1 22.2 - - - +
1269A ASP* 4.7 0.7 - - - +
237B ASN* 4.1 26.9 - - - +
281B ASP 5.7 0.4 + - - -
284B ALA* 5.2 4.0 - - - +
285B VAL* 3.3 45.7 - - - +
288B GLU* 5.2 3.0 - - - +
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Residues in contact with ALA1266 (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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1216A LYS* 3.9 32.1 - - + -
1262A GLN* 2.9 16.0 + - - +
1265A ARG* 1.3 76.5 - - + +
1267A LEU* 1.3 61.6 + - - +
1269A ASP* 2.4 43.3 + - + +
1270A VAL* 3.5 8.0 + - + +
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Residues in contact with LEU1267 (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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1166A LEU* 3.7 18.4 - - + +
1173A VAL* 5.4 4.3 - - + -
1184A ILE* 4.4 23.1 - - + -
1186A VAL* 4.8 11.2 - - + -
1209A ILE* 4.6 27.8 - - + -
1217A ILE* 5.1 15.5 - - + -
1230A ILE* 4.7 13.0 - - + -
1232A ILE* 5.3 6.3 - - + -
1262A GLN 4.2 0.4 + - - -
1263A LEU* 3.0 27.6 + - + +
1264A ARG* 6.0 0.2 - - - -
1266A ALA* 1.3 72.9 - - - +
1268A PRO* 1.3 61.3 - - + +
1269A ASP 2.8 11.1 + - - -
1270A VAL* 3.7 19.2 + - + +
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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