Contacts of the helix formed by residues 1257 - 1270 (chain A) in PDB entry 3RZD
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 ASP1257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1152A ILE* 5.4 3.1 - - - +
1191A TRP* 3.5 45.3 + - - +
1256A GLU* 1.4 77.9 + - - +
1258A HIS* 1.4 59.1 + - - +
1259A MET* 3.3 1.7 - - - +
1260A LEU* 3.5 11.0 + - - +
1261A LYS* 3.0 31.5 + - - +
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Residues in contact with HIS1258 (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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1256A GLU 2.7 12.9 + - - +
1257A ASP* 1.4 71.1 - - - +
1259A MET* 1.4 61.3 + - - +
1261A LYS* 3.8 6.2 + - + +
1262A LYS* 3.3 49.7 + - + +
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Residues in contact with MET1259 (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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1223A ASP* 4.5 21.3 - - - +
1242A VAL* 4.4 22.9 - - + -
1255A GLU 4.4 16.1 + - - +
1256A GLU* 3.9 9.4 + - + -
1257A ASP 3.3 0.2 - - - -
1258A HIS* 1.4 79.8 - - - +
1260A LEU* 1.4 57.5 + - - +
1262A LYS* 3.5 5.1 + - - +
1263A ILE* 3.2 40.4 + - + +
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Residues in contact with LEU1260 (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 ILE* 3.8 28.7 - - + -
1191A TRP* 4.5 17.9 - - + +
1192A LEU 3.7 25.8 - - - +
1193A LEU* 3.8 26.0 - - + +
1224A LEU* 5.9 1.8 - - + -
1240A CYS* 4.9 4.3 - - + +
1241A ARG* 5.2 0.9 - - - -
1242A VAL* 3.9 33.7 - - + +
1256A GLU* 6.1 0.2 - - - +
1257A ASP* 3.5 12.0 + - - +
1259A MET* 1.4 74.3 - - - +
1261A LYS* 1.4 61.0 + - - +
1262A LYS 3.1 2.2 - - - -
1263A ILE* 2.9 27.7 + - + +
1264A GLU* 3.1 14.2 + - - +
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Residues in contact with LYS1261 (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 ILE* 3.8 21.6 - - + +
1257A ASP 3.0 19.0 + - - +
1258A HIS* 4.2 7.0 - - + +
1260A LEU* 1.4 75.0 - - - +
1262A LYS* 1.4 58.8 + - + +
1264A GLU* 3.3 41.0 + - + +
1265A ASN* 3.7 6.4 + - - +
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Residues in contact with LYS1262 (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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1258A HIS* 3.3 46.2 + - + +
1259A MET* 3.7 5.4 - - - +
1260A LEU 3.1 0.8 - - - -
1261A LYS* 1.4 75.3 - - + +
1263A ILE* 1.4 60.4 + - + +
1264A GLU 3.4 0.2 - - - -
1265A ASN* 3.4 23.4 + - + +
1266A THR* 2.8 32.7 + - - -
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Residues in contact with ILE1263 (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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1193A LEU* 4.2 12.6 - - + -
1220A PHE* 3.9 32.9 - - + -
1223A ASP* 5.0 2.9 - - - +
1224A LEU* 3.9 34.1 - - + -
1242A VAL* 5.2 4.0 - - + -
1259A MET* 3.2 35.5 + - + +
1260A LEU* 2.9 15.3 + - + +
1262A LYS* 1.4 75.6 - - + +
1264A GLU* 1.4 58.1 - - - +
1266A THR* 3.2 9.5 + - - +
1267A MET* 2.9 28.8 + - - +
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Residues in contact with GLU1264 (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 SER* 2.8 27.8 + - - +
1152A ILE* 5.0 4.7 - - + -
1193A LEU* 3.8 32.1 - - + +
1195A LEU* 5.5 1.6 - - + -
1260A LEU 3.1 6.9 + - - +
1261A LYS* 3.3 40.6 + - + +
1263A ILE* 1.4 76.2 - - - +
1265A ASN* 1.3 69.6 + - - +
1267A MET* 3.4 7.9 - - - +
1268A LEU* 3.1 53.8 + - + +
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Residues in contact with ASN1265 (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 LYS* 3.7 13.0 + - - +
1262A LYS* 3.4 28.4 + - - +
1263A ILE 3.2 0.2 - - - -
1264A GLU* 1.3 89.2 - - - +
1266A THR* 1.4 61.1 + - - +
1268A LEU* 5.2 2.9 - - - -
1269A GLU* 3.3 37.0 + - - +
1270A ASN* 5.2 0.3 + - - -
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Residues in contact with THR1266 (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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1219A THR* 5.7 1.3 - - + -
1220A PHE* 5.0 15.3 - - + -
1262A LYS 2.8 16.3 + - - -
1263A ILE* 3.5 11.7 - - + +
1265A ASN* 1.4 74.2 + - - +
1267A MET* 1.4 59.5 + - - +
1270A ASN* 2.7 56.1 + - + +
1271A ILE* 3.6 7.4 - - + +
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Residues in contact with MET1267 (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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1143A LEU* 3.4 23.7 - - + +
1193A LEU* 3.7 29.8 - - - -
1195A LEU* 3.7 29.8 - - + -
1216A ILE* 3.7 35.2 - - + -
1220A PHE* 4.0 18.4 - - + -
1224A LEU* 5.0 0.7 - - - -
1240A CYS* 4.4 10.8 - - - -
1263A ILE* 2.9 19.3 + - - +
1264A GLU* 3.4 10.5 - - - +
1266A THR* 1.4 75.7 - - - +
1268A LEU* 1.3 63.8 + - + +
1271A ILE* 3.3 31.9 + - + +
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Residues in contact with LEU1268 (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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1142A THR* 2.8 27.7 + - - -
1143A LEU* 4.4 5.4 - - + -
1144A LYS* 3.4 33.9 + - + +
1147A THR* 4.0 31.9 - - + +
1150A SER* 4.6 10.5 - - - +
1195A LEU* 5.4 3.6 - - + -
1264A GLU* 3.1 39.4 + - + +
1265A ASN* 4.5 1.8 - - - +
1267A MET* 1.3 82.1 - - + +
1269A GLU* 1.3 71.8 + - - +
1271A ILE 4.8 0.2 + - - -
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Residues in contact with GLU1269 (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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1142A THR* 4.6 5.1 + - - -
1144A LYS* 3.4 32.1 + - - +
1265A ASN* 3.3 26.2 + - - +
1268A LEU* 1.3 95.9 - - - +
1270A ASN* 1.3 72.8 + - - +
1271A ILE 3.6 2.3 + - - -
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Residues in contact with ASN1270 (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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1265A ASN 5.2 0.4 + - - -
1266A THR* 2.7 37.7 + - + +
1269A GLU* 1.3 87.2 - - - +
1271A ILE* 1.3 65.3 + - - +
1272A THR* 4.1 2.0 + - - -
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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