Contacts of the strand formed by residues 1254 - 1268 (chain A) in PDB entry 2QOM
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 LYS1254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1232A ASP 3.5 4.5 - - - +
1233A LEU* 4.5 18.8 - - + -
1250A ILE* 4.6 2.3 - - - +
1252A GLY 3.9 0.2 - - - -
1253A GLU* 1.3 91.0 - - + +
1255A ASP* 1.3 62.9 + - - +
1285A LYS* 2.9 28.2 + - - +
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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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1230A GLN 4.6 0.2 - - - -
1231A PHE* 3.4 5.2 - - - +
1232A ASP* 3.3 42.3 + - - +
1250A ILE* 4.0 10.3 - - + +
1254A LYS* 1.3 77.7 - - - +
1256A SER* 1.3 70.0 + - - +
1257A ARG* 2.8 26.5 + - - +
1284A GLY* 3.7 2.6 - - - -
1285A LYS* 2.8 39.2 + - + +
1286A TYR* 3.2 18.5 + - - +
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Residues in contact with SER1256 (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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1229A TYR* 6.4 1.3 - - - -
1230A GLN 3.3 5.8 - - - -
1231A PHE* 3.8 26.0 - - - -
1255A ASP* 1.3 81.0 + - - +
1257A ARG* 1.3 63.6 + - - +
1283A PHE* 3.5 8.7 - - - +
1284A GLY* 3.4 16.6 - - - -
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Residues in contact with ARG1257 (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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1229A TYR* 3.5 11.3 - - - +
1230A GLN* 2.9 63.7 + - + +
1232A ASP* 3.2 36.4 + - - -
1250A ILE* 5.1 2.0 - - - +
1255A ASP* 2.8 22.5 + - - +
1256A SER* 1.3 74.4 - - - +
1258A MET* 1.3 60.7 + - - +
1259A LEU* 4.7 6.5 - - + -
1281A SER* 3.5 22.4 - - - +
1282A ALA 3.6 4.7 - - - +
1283A PHE* 5.6 0.4 - - - -
1284A GLY* 3.7 11.7 - - - -
1286A TYR* 2.8 48.9 + - - +
1287A ASN* 3.7 6.7 - - - +
1288A VAL* 4.8 4.0 - - - +
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Residues in contact with MET1258 (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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1227A LEU* 4.0 10.3 - - + -
1228A GLY 3.6 11.0 - - - +
1229A TYR* 4.2 14.3 - - + -
1257A ARG* 1.3 71.9 - - - +
1259A LEU* 1.3 65.4 + - - +
1260A MET* 3.3 41.2 - - + +
1281A SER* 3.1 8.7 - - - -
1282A ALA* 3.0 36.1 + - + +
1283A PHE* 4.0 27.3 - - + +
1210B VAL* 3.8 28.7 - - + -
1225B ALA* 4.9 13.0 - - + -
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Residues in contact with LEU1259 (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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1205A ARG* 3.8 32.3 - - + +
1226A GLY 5.3 0.2 - - - -
1227A LEU* 3.3 15.4 - - - +
1228A GLY* 2.8 41.6 + - - +
1229A TYR 4.7 2.5 - - - -
1230A GLN* 4.0 37.2 - - + +
1257A ARG* 4.7 4.0 - - + -
1258A MET* 1.3 74.1 - - - +
1260A MET* 1.3 61.8 + - - +
1261A SER* 6.3 0.4 - - - -
1279A GLU* 6.4 1.6 - - + -
1280A LYS 4.0 3.8 - - - +
1281A SER* 4.0 20.2 - - - -
1288A VAL* 5.9 4.3 - - + -
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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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1226A GLY 3.7 4.9 - - - -
1227A LEU* 4.1 7.2 - - + -
1258A MET* 3.3 34.5 - - + +
1259A LEU* 1.3 74.2 - - - +
1261A SER* 1.3 63.2 + - - +
1279A GLU* 3.5 2.9 - - - +
1280A LYS* 3.1 60.8 + - + +
1281A SER 4.9 0.7 - - - -
1282A ALA* 4.9 13.5 - - - -
1227B LEU* 5.6 3.8 - - + -
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Residues in contact with SER1261 (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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1209A ASP* 4.8 6.6 + - - -
1225A ALA* 3.3 5.4 - - - +
1226A GLY* 3.0 44.2 + - - +
1259A LEU* 6.3 0.7 - - - -
1260A MET* 1.3 75.5 - - - +
1262A VAL* 1.3 63.5 + - - +
1277A GLU* 3.8 11.9 + - - -
1278A PHE 3.4 6.5 - - - -
1279A GLU* 3.8 20.9 - - - -
1227B LEU* 4.1 4.9 - - - +
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Residues in contact with VAL1262 (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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1224A ARG 3.5 12.8 - - - +
1225A ALA* 4.2 2.7 - - + +
1261A SER* 1.3 76.7 - - - +
1263A GLY* 1.3 63.3 + - - +
1264A LEU* 5.9 2.0 - - + -
1277A GLU* 3.5 4.3 - - - -
1278A PHE* 2.8 54.7 + - + +
1227B LEU* 6.1 1.1 - - + -
1229B TYR* 4.6 7.4 - - - +
1258B MET* 4.6 16.2 - - + -
1283B PHE* 5.5 8.3 - - + -
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Residues in contact with GLY1263 (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 ALA* 3.6 1.0 - - - -
1224A ARG* 2.7 50.1 + - - +
1262A VAL* 1.3 77.9 - - - +
1264A LEU* 1.3 72.6 + - - +
1276A LEU* 3.2 13.7 - - - -
1277A GLU* 3.7 8.7 + - - -
1278A PHE* 5.9 1.1 - - - -
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Residues in contact with LEU1264 (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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1221A VAL* 4.9 17.0 - - + -
1222A THR 3.4 8.1 - - - +
1223A ALA* 5.0 7.0 - - + -
1224A ARG* 5.0 2.9 - - - -
1262A VAL* 5.9 2.5 - - + -
1263A GLY* 1.3 87.3 - - - +
1265A ASN* 1.3 68.5 + - - +
1266A ALA* 4.0 4.5 - - + +
1274A PHE* 5.7 10.5 - - + -
1275A GLY* 3.1 23.0 - - - -
1276A LEU* 2.8 33.8 + - + +
1277A GLU* 5.2 1.0 - - - +
1278A PHE* 6.4 1.3 - - + -
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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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1026A ASN* 3.3 19.9 + - - +
1030A GLY* 4.3 2.4 - - - -
1031A ASP* 3.3 40.7 - - + +
1166A TRP* 5.3 0.2 - - - -
1220A LYS 3.8 0.7 - - - +
1221A VAL* 3.3 3.7 + - - -
1222A THR* 2.8 47.6 + - - +
1224A ARG* 3.0 30.9 + - - +
1264A LEU* 1.3 82.6 + - - +
1266A ALA* 1.3 62.6 + - - +
1267A GLU* 5.2 0.3 - - - +
1274A PHE 3.9 2.4 + - - -
1275A GLY* 4.3 8.3 - - - -
1295A ASN* 4.9 0.8 - - - +
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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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1031A ASP* 6.1 0.2 - - - +
1220A LYS 3.5 4.9 - - - -
1221A VAL* 4.2 14.6 - - + -
1264A LEU* 4.0 4.2 - - + +
1265A ASN* 1.3 76.9 - - - +
1267A GLU* 1.3 63.4 + - - +
1268A ILE* 5.3 2.7 - - + -
1273A ARG* 3.6 8.0 - - - +
1274A PHE* 2.7 75.4 + - + +
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Residues in contact with GLU1267 (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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1031A ASP* 5.6 4.3 - - - +
1218A ASP 3.6 1.7 - - - +
1219A TRP* 3.2 6.9 - - - +
1220A LYS* 2.8 71.7 + - + +
1265A ASN 5.2 0.4 - - - +
1266A ALA* 1.3 77.3 - - - +
1268A ILE* 1.3 63.5 + - - +
1269A ARG 4.2 10.7 - - - +
1272A VAL 4.0 3.4 - - - -
1273A ARG* 4.1 41.8 + - + +
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Residues in contact with ILE1268 (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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1218A ASP* 4.1 1.1 - - + -
1219A TRP* 4.7 8.1 - - + +
1266A ALA* 5.3 0.9 - - + -
1267A GLU* 1.3 79.8 - - - +
1269A ARG* 1.3 100.0 + - + +
1270A ASP 3.2 3.6 + - - -
1271A ASN 3.8 0.3 + - - -
1272A VAL* 2.8 47.5 + - + +
1274A PHE* 4.5 23.3 - - + -
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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