Contacts of the helix formed by residues 1301 - 1306 (chain A) in PDB entry 6CNB
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 ARG1301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1299A GLY 2.5 16.5 + - - +
1300A LEU* 1.3 74.8 - - - +
1302A ASP* 1.3 61.6 + - - +
1304A MET* 3.2 7.9 - - - +
1305A CYS* 2.8 28.5 + - + +
1324A SER* 3.1 28.3 + - - -
1325A VAL* 3.4 28.1 + - + +
136E ASN* 5.9 2.2 - - - +
138E ALA* 5.3 11.0 - - + +
139E ALA* 3.8 36.1 + - - +
141E VAL* 5.0 3.9 - - + +
183E PRO* 6.0 1.4 - - - +
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Residues in contact with ASP1302 (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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1275A LEU* 3.2 34.1 - - + +
1276A PRO* 5.4 2.4 - - - +
1277A ASP* 5.8 3.3 + - - +
1278A ILE* 5.0 1.8 - - - +
1299A GLY* 3.3 31.4 - - - -
1300A LEU 3.5 0.3 + - - -
1301A ARG* 1.3 77.4 - - - +
1303A VAL* 1.3 60.5 + - - +
1305A CYS* 2.8 11.6 + - - +
1306A THR* 2.6 38.9 + - - +
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Residues in contact with VAL1303 (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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1141A ILE* 4.4 22.4 - - + -
1143A ALA* 5.2 10.8 - - + -
1161A VAL* 5.1 6.7 - - + -
1275A LEU* 3.6 11.0 - - + +
1278A ILE* 4.6 13.9 - - + -
1293A LEU* 5.9 2.0 - - + -
1295A VAL* 5.4 11.4 - - + -
1299A GLY* 5.0 0.7 - - - -
1300A LEU* 3.4 31.0 - - + +
1302A ASP* 1.3 83.3 + - - +
1304A MET* 1.3 68.2 + - - +
1306A THR* 3.3 18.7 + - - +
1309A VAL* 3.5 18.1 - - + +
1314A THR* 5.4 2.9 - - + +
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Residues in contact with MET1304 (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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1300A LEU* 3.0 41.7 - - + +
1301A ARG* 3.2 8.7 + - - +
1302A ASP 3.1 0.4 - - - -
1303A VAL* 1.3 86.1 - - + +
1305A CYS* 1.3 62.0 + - - +
1306A THR 4.0 3.6 - - - +
1309A VAL* 4.1 11.8 - - - +
1311A GLY* 4.1 15.6 - - - +
1314A THR* 3.1 37.5 - - - +
1325A VAL* 5.2 2.9 - - + -
1326A LEU* 3.7 30.1 - - + -
141E VAL* 5.6 0.9 - - + -
142E VAL* 3.4 36.3 - - + +
144E ILE* 4.6 4.9 - - - -
147E HIS* 4.1 8.7 - - + +
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Residues in contact with CYS1305 (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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1301A ARG* 2.8 13.1 + - + +
1302A ASP* 2.8 17.1 + - - +
1304A MET* 1.3 72.7 - - - +
1306A THR* 1.3 65.3 + - - +
1307A ASP* 3.3 4.2 + - - -
11E ARG* 2.7 41.5 - - - +
14E ARG* 5.0 13.2 + - - +
138E ALA* 5.3 1.1 - - + +
141E VAL* 3.4 43.2 - - + +
142E VAL* 5.3 1.6 - - - -
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Residues in contact with THR1306 (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* 5.5 2.0 - - + +
1160A ARG* 4.4 15.3 - - + +
1161A VAL* 3.6 21.5 - - + +
1275A LEU* 3.7 13.8 - - + +
1302A ASP* 2.6 27.9 + - - +
1303A VAL* 3.3 19.4 - - - -
1304A MET 3.3 1.6 - - - -
1305A CYS* 1.3 76.4 - - - +
1307A ASP* 1.3 74.7 + - + +
1308A GLY 3.6 0.3 + - - -
1309A VAL* 3.1 26.2 + - + +
11E ARG* 5.7 0.9 - - - +
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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