Contacts of the strand formed by residues 1281 - 1290 (chain B) in PDB entry 3GIJ
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 PRO1281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1273B TYR* 4.0 11.4 - - + +
1276B LEU* 3.9 15.0 - - + -
1279B ARG 3.6 8.7 - - - +
1280B ILE* 1.3 88.7 - - + +
1282B LYS* 1.3 56.5 + - - +
1283B ALA 3.9 2.2 - - - +
1305B GLY* 3.3 1.6 - - - -
1306B ILE* 2.7 45.9 + - + +
1337B PHE* 3.5 42.4 - - + -
1338B SER 3.5 13.9 - - - +
1340B PHE* 3.6 11.4 - - + -
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Residues in contact with LYS1282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281B PRO* 1.3 74.6 - - - +
1283B ALA* 1.3 57.4 + - - +
1301B THR* 3.4 4.4 - - + -
1302B PHE* 2.6 48.2 + - - +
1303B PRO 4.5 4.5 - - - +
1304B HIS* 3.3 33.9 - - - +
1305B GLY 3.9 2.0 - - - +
1306B ILE* 3.6 6.1 - - - +
1338B SER 3.1 0.2 + - - -
1339B LYS* 2.9 35.1 + - + +
1340B PHE 4.7 1.9 + - - -
1341B ILE* 3.9 31.3 + - + +
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Residues in contact with ALA1283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281B PRO* 3.9 0.9 - - - +
1282B LYS* 1.3 79.5 - - - +
1284B ILE* 1.3 59.9 + - - +
1285B HIS* 4.3 7.9 - - - +
1300B ARG 3.2 5.2 - - - +
1301B THR* 3.5 21.5 - - - +
1306B ILE* 3.5 4.1 - - - +
1337B PHE* 3.4 11.1 - - - -
1338B SER* 3.0 49.5 + - - +
1339B LYS* 3.7 13.2 - - + -
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Residues in contact with ILE1284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283B ALA* 1.3 73.6 - - - +
1285B HIS* 1.3 64.8 - - - +
1299B GLY* 2.9 2.4 - - - -
1300B ARG 2.7 45.3 + - - +
1302B PHE* 3.9 2.2 - - + -
1306B ILE* 3.7 14.1 - - + -
1311B ALA* 3.7 26.2 - - - +
1314B GLU* 3.7 25.8 - - + -
1315B SER* 3.8 18.4 - - - +
1318B LEU* 3.4 6.5 - - + +
1335B VAL* 3.5 28.7 - - + -
1336B ARG 3.4 3.6 - - - -
1337B PHE* 3.7 22.2 - - + -
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Residues in contact with HIS1285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283B ALA* 4.3 8.5 - - - +
1284B ILE* 1.3 81.6 + - - +
1286B VAL* 1.3 63.5 + - - +
1287B VAL* 3.5 9.6 + - + +
1297B SER* 4.4 11.0 + - - -
1298B ARG 3.1 8.2 - - - +
1299B GLY* 3.3 24.2 + - - -
1301B THR* 5.1 0.6 + - - -
1335B VAL* 3.3 4.7 - - - +
1336B ARG* 2.8 49.7 + - + +
1338B SER* 4.0 21.6 + - - -
1339B LYS* 5.7 2.4 - - - -
1807H A 4.5 14.5 + - + -
1808H T 3.3 35.0 + - + +
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Residues in contact with VAL1286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1265B LEU* 3.6 23.1 - - + -
1284B ILE* 4.5 2.9 - - + -
1285B HIS* 1.3 71.7 - - - +
1287B VAL* 1.3 60.8 + - - +
1297B SER* 3.3 0.3 - - - -
1298B ARG 2.6 30.2 + - - -
1315B SER* 3.2 41.7 - - - +
1318B LEU* 3.4 22.8 - - + +
1319B LEU* 4.2 11.2 - - - -
1322B ILE* 3.2 17.3 - - + +
1333B ILE* 3.6 19.3 - - + -
1334B GLY 3.6 2.7 - - - -
1335B VAL* 4.5 1.1 - - + -
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Residues in contact with VAL1287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248B ILE* 3.6 23.2 - - + +
1285B HIS* 3.5 11.4 + - + +
1286B VAL* 1.3 74.3 - - - +
1288B ALA* 1.3 60.5 + - - +
1289B VAL* 4.9 1.1 - - + -
1295B ILE* 3.5 29.6 - - + -
1296B VAL 3.4 2.9 - - - -
1297B SER* 3.8 15.0 - - - -
1333B ILE* 3.5 3.1 - - - +
1334B GLY 2.8 39.9 + - - +
1335B VAL 4.7 0.9 - - - +
1336B ARG* 4.4 20.4 - - + +
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Residues in contact with ALA1288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286B VAL 3.7 0.6 + - - -
1287B VAL* 1.3 73.8 - - - +
1289B VAL* 1.3 62.6 + - - +
1290B THR* 3.6 3.2 + - + +
1294B ASP 3.6 0.3 - - - +
1295B ILE* 3.3 2.3 - - - +
1296B VAL* 2.6 45.8 + - + +
1322B ILE* 3.8 30.7 - - + -
1330B ILE* 3.9 24.5 - - + -
1332B ARG 3.5 3.8 - - - -
1333B ILE* 4.0 4.9 - - + -
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Residues in contact with VAL1289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248B ILE* 3.9 17.5 - - + -
1288B ALA* 1.3 73.2 - - - +
1290B THR* 1.3 62.9 + - - +
1293B LEU* 3.9 26.5 - - + +
1294B ASP 3.1 8.5 - - - +
1295B ILE* 4.0 20.9 - - + -
1330B ILE* 3.5 2.2 - - - +
1331B ARG* 2.5 34.4 + - + -
1332B ARG* 2.5 49.4 + - + +
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Residues in contact with THR1290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288B ALA* 4.5 6.7 - - + +
1289B VAL* 1.3 81.2 - - - +
1291B GLU* 1.3 66.4 + - - +
1292B ASP* 2.7 24.9 + - - -
1293B LEU* 2.9 14.4 + - - -
1294B ASP* 2.5 30.1 + - - +
1296B VAL* 4.0 14.4 - - + -
1322B ILE* 6.1 1.3 - - + -
1326B ASP* 3.7 22.2 - - - +
1328B ARG* 3.8 20.0 - - + +
1329B LYS 3.2 8.7 - - - +
1330B ILE* 4.1 4.3 - - + +
1331B ARG* 3.7 4.5 - - - +
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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