Contacts of the strand formed by residues 1387 - 1398 (chain G) in PDB entry 2VKZ
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 GLY1387 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1383G ASN* 4.9 0.7 - - - -
1384G GLN* 2.7 41.2 + - - +
1386G THR* 1.3 83.1 - - - +
1388G LYS* 1.3 59.1 + - - -
1389G ILE 4.0 0.2 + - - -
1411G PHE* 3.4 10.0 - - - -
1412G TYR 3.4 9.6 - - - -
1414G GLY 3.1 14.8 - - - -
1416G TYR* 4.5 4.0 - - - -
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Residues in contact with LYS1388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342G THR 3.7 3.2 + - - -
1343G VAL* 3.7 32.3 - - + +
1344G ASP 4.5 2.5 - - - +
1381G VAL* 3.5 28.2 - - + +
1382G VAL 3.6 5.8 - - - +
1383G ASN* 3.1 24.7 + - - +
1387G GLY* 1.3 73.0 - - - -
1389G ILE* 1.3 63.2 + - - +
1390G VAL* 5.0 3.0 - - + +
1410G PHE 3.9 0.3 - - - +
1411G PHE* 3.1 6.8 - - - -
1412G TYR* 2.8 50.8 + - + +
1416G TYR* 3.9 24.7 - - + -
1418G ASP* 2.9 30.2 + - - -
1421G ASN 3.8 10.3 + - - -
1422G THR* 5.6 1.0 + - - +
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Residues in contact with ILE1389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353G LEU* 3.9 21.5 - - + -
1380G SER* 3.5 1.1 - - - +
1381G VAL* 3.1 5.7 - - - +
1382G VAL* 2.9 49.0 + - + +
1384G GLN* 3.3 32.1 - - - +
1387G GLY 4.0 0.2 + - - -
1388G LYS* 1.3 71.3 - - - +
1390G VAL* 1.3 65.8 + - - +
1391G ASP* 3.9 24.2 - - - +
1409G SER* 5.2 0.7 - - - -
1410G PHE 3.5 7.2 - - - +
1411G PHE* 3.3 24.9 - - + -
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Residues in contact with VAL1390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337G ALA 4.5 3.1 - - - +
1338G ILE* 4.0 27.8 - - + -
1343G VAL* 4.1 17.7 - - + -
1378G ILE* 3.6 34.8 - - + -
1380G SER 3.4 1.3 - - - -
1381G VAL* 3.7 17.7 - - + -
1388G LYS* 5.0 3.6 - - + -
1389G ILE* 1.3 81.2 - - - +
1391G ASP* 1.3 64.4 + - - +
1392G VAL* 4.0 7.6 + - + -
1408G SER 3.9 0.9 - - - +
1409G SER* 3.1 3.6 - - - -
1410G PHE* 2.8 40.9 + - - +
1412G TYR* 5.0 7.4 - - + -
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Residues in contact with ASP1391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378G ILE* 3.4 3.5 - - - +
1379G GLU* 2.7 46.6 + - - +
1380G SER* 2.7 36.5 + - - +
1389G ILE* 3.9 14.3 - - - +
1390G VAL* 1.3 73.4 - - - +
1392G VAL* 1.3 56.3 + - - +
1393G VAL* 6.3 0.2 - - + -
1407G THR* 6.2 2.9 - - + -
1408G SER 3.6 3.6 - - - +
1409G SER* 2.9 25.4 - - - -
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Residues in contact with VAL1392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334G ILE* 3.8 28.0 - - + +
1337G ALA* 3.7 30.7 - - + -
1338G ILE* 4.9 1.6 - - + -
1376G ALA* 4.4 7.2 - - + -
1377G VAL 3.7 13.0 - - - +
1378G ILE* 4.2 1.1 - - + -
1390G VAL* 4.2 11.7 - - + +
1391G ASP* 1.3 77.6 - - - +
1393G VAL* 1.3 70.3 + - - +
1394G GLY 4.3 0.2 - - - -
1406G VAL 4.5 0.2 - - - -
1407G THR* 3.6 5.5 - - - +
1408G SER 2.7 37.8 + - - +
1410G PHE* 3.9 25.1 - - + -
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Residues in contact with VAL1393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334G ILE* 5.4 0.2 - - - -
1375G THR 3.5 1.2 - - - +
1376G ALA* 3.3 2.9 - - - -
1377G VAL* 2.6 51.5 + - + +
1379G GLU* 4.5 24.9 - - + +
1391G ASP 5.6 0.2 - - - -
1392G VAL* 1.3 81.4 - - - +
1394G GLY* 1.3 73.5 + - - +
1395G THR* 4.2 7.6 - - - +
1405G GLU* 4.6 16.6 - - + +
1406G VAL 3.4 4.7 - - - +
1407G THR* 4.7 12.1 - - + +
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Residues in contact with GLY1394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334G ILE* 4.7 12.3 - - - +
1374G THR* 5.3 2.0 - - - -
1375G THR 3.3 6.5 - - - -
1376G ALA* 4.3 4.5 - - - -
1392G VAL 4.3 0.2 - - - -
1393G VAL* 1.3 78.3 - - - +
1395G THR* 1.3 65.0 + - - -
1396G LEU* 4.1 5.8 - - - -
1405G GLU* 3.2 5.4 - - - -
1406G VAL* 2.7 43.8 + - - -
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Residues in contact with THR1395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360G ILE* 6.3 0.7 - - + -
1373G SER 3.6 1.2 - - - +
1375G THR* 2.8 39.3 + - - +
1377G VAL* 6.2 0.3 - - - +
1393G VAL* 4.2 6.2 - - - +
1394G GLY* 1.3 74.9 + - - -
1396G LEU* 1.3 63.2 - - - +
1397G SER* 3.4 18.6 + - - +
1402G PRO* 4.2 21.5 - - + -
1404G MET 3.7 7.6 - - - +
1405G GLU* 3.7 17.8 + - + +
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Residues in contact with LEU1396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326G ALA* 3.5 42.4 - - + +
1329G VAL* 4.3 6.5 - - + -
1330G GLY* 4.7 2.0 - - - -
1334G ILE* 6.3 0.2 - - + -
1366G LEU* 4.5 9.2 - - + -
1372G VAL* 3.8 22.9 - - + -
1373G SER 3.4 5.2 - - - -
1374G THR* 3.4 27.6 - - + +
1394G GLY* 4.8 1.3 - - - -
1395G THR* 1.3 75.0 - - - +
1397G SER* 1.3 54.8 + - - +
1402G PRO* 3.8 0.5 - - - +
1403G VAL* 2.7 32.8 + - + +
1404G MET* 3.0 28.7 + - + +
1406G VAL* 4.3 18.8 - - + -
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Residues in contact with SER1397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372G VAL* 3.4 10.0 - - - +
1373G SER* 2.8 41.3 + - - -
1375G THR* 5.6 1.7 + - - -
1395G THR* 3.5 19.4 + - - +
1396G LEU* 1.3 75.2 - - - +
1398G ARG* 1.3 60.9 + - - +
1400G GLY 4.4 9.6 - - - -
1401G LYS 3.3 15.9 - - - -
1402G PRO* 3.8 7.8 - - - +
1403G VAL* 4.5 0.2 - - - -
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Residues in contact with ARG1398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363G ALA* 4.9 1.2 - - - +
1364G LYS* 3.0 34.0 + - - +
1365G PRO 2.8 32.5 + - - -
1366G LEU* 3.7 9.6 - - + +
1367G GLN* 5.8 0.4 - - - +
1370G ASP* 2.8 33.6 + - + +
1371G VAL 4.0 16.2 - - - +
1372G VAL* 5.3 3.8 - - + -
1373G SER* 5.8 0.7 - - - -
1397G SER* 1.3 75.3 - - - +
1399G ASN* 1.3 92.3 + - - +
1400G GLY 3.3 0.7 - - - -
1401G LYS* 2.7 24.1 + - - +
1403G VAL* 3.3 28.9 - - + +
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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