Contacts of the strand formed by residues 1387 - 1398 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382I VAL 3.9 0.2 - - - +
1383I ASN* 4.8 0.9 - - - -
1384I GLN* 2.7 40.9 + - - +
1386I THR* 1.3 83.9 - - - +
1388I LYS* 1.3 59.1 + - - -
1389I ILE 4.0 0.2 + - - -
1411I PHE* 3.5 8.7 - - - -
1412I TYR 3.4 10.5 - - - -
1414I GLY 3.1 14.1 - - - -
1416I TYR* 4.4 3.8 - - - -
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Residues in contact with LYS1388 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342I THR 3.8 3.0 + - - -
1343I VAL* 3.6 32.0 - - + +
1344I ASP 4.5 2.2 - - - +
1381I VAL* 3.5 27.9 - - + +
1382I VAL 3.6 5.2 - - - +
1383I ASN* 3.2 25.1 - - - +
1387I GLY* 1.3 73.2 - - - -
1389I ILE* 1.3 62.0 + - - +
1390I VAL* 5.0 2.4 - - + +
1410I PHE 3.9 0.2 - - - +
1411I PHE* 3.1 6.6 - - - -
1412I TYR* 2.8 51.5 + - + +
1416I TYR* 3.9 25.7 - - + -
1418I ASP* 2.9 30.6 + - - -
1421I ASN 3.9 9.3 + - - -
1422I THR* 5.6 1.0 + - - +
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Residues in contact with ILE1389 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353I LEU* 3.9 21.1 - - + -
1380I SER* 3.5 1.2 - - - +
1381I VAL* 3.1 6.1 - - - +
1382I VAL* 2.9 49.1 + - + +
1384I GLN* 3.4 31.6 - - - +
1387I GLY 4.0 0.2 + - - -
1388I LYS* 1.3 72.2 - - - +
1390I VAL* 1.3 66.5 + - - +
1391I ASP* 3.8 24.5 - - - +
1409I SER* 5.2 0.4 - - - -
1410I PHE 3.5 7.2 - - - +
1411I PHE* 3.3 24.2 - - + -
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Residues in contact with VAL1390 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337I ALA 4.5 2.9 - - - +
1338I ILE* 4.0 28.5 - - + -
1343I VAL* 4.1 17.0 - - + -
1378I ILE* 3.7 33.7 - - + -
1380I SER 3.4 1.3 - - - -
1381I VAL* 3.7 17.7 - - + -
1388I LYS* 5.0 3.1 - - + -
1389I ILE* 1.3 80.3 - - - +
1391I ASP* 1.3 64.0 - - - +
1392I VAL* 3.9 8.0 + - + -
1408I SER 3.8 0.9 - - - +
1409I SER* 3.1 3.1 - - - -
1410I PHE* 2.8 41.6 + - - +
1412I TYR* 5.0 7.4 - - + -
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Residues in contact with ASP1391 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1378I ILE* 3.5 3.8 - - - +
1379I GLU* 2.7 45.1 + - - +
1380I SER* 2.7 37.3 + - - +
1389I ILE* 3.8 13.9 - - - +
1390I VAL* 1.3 74.0 - - - +
1392I VAL* 1.3 56.5 + - - +
1407I THR* 6.2 2.5 - - + -
1408I SER 3.6 3.6 - - - -
1409I SER* 2.9 25.8 - - - -
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Residues in contact with VAL1392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334I ILE* 3.7 28.9 - - + +
1337I ALA* 3.7 31.9 - - + -
1338I ILE* 4.9 1.3 - - + -
1376I ALA* 4.4 7.0 - - + -
1377I VAL 3.7 13.2 - - - +
1378I ILE* 4.2 1.3 - - + +
1390I VAL* 4.2 11.2 - - + +
1391I ASP* 1.3 77.9 - - - +
1393I VAL* 1.3 71.4 + - - +
1406I VAL 4.5 0.2 - - - -
1407I THR* 3.7 5.5 - - - +
1408I SER 2.7 41.1 + - - +
1410I PHE* 3.9 24.5 - - + -
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Residues in contact with VAL1393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375I THR 3.6 1.4 - - - +
1376I ALA* 3.2 3.0 - - - -
1377I VAL* 2.6 51.1 + - + +
1379I GLU* 4.5 24.7 - - + +
1392I VAL* 1.3 82.5 - - - +
1394I GLY* 1.3 74.3 + - - +
1395I THR* 4.2 8.5 - - - +
1405I GLU* 4.5 16.2 - - + +
1406I VAL 3.4 4.9 - - - +
1407I THR* 4.6 12.6 - - + +
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Residues in contact with GLY1394 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334I ILE* 4.7 13.0 - - - +
1374I THR* 5.3 2.0 - - - -
1375I THR 3.3 7.2 - - - -
1376I ALA* 4.2 3.8 - - - -
1392I VAL 4.3 0.2 - - - -
1393I VAL* 1.3 78.8 - - - +
1395I THR* 1.3 65.8 + - - -
1396I LEU* 4.1 6.3 - - - -
1405I GLU* 3.2 5.5 - - - -
1406I VAL* 2.7 43.5 + - - -
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Residues in contact with THR1395 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360I ILE* 6.3 0.4 - - + -
1373I SER 3.6 1.2 - - - +
1375I THR* 2.8 38.7 + - - +
1377I VAL* 6.1 0.5 - - - +
1393I VAL* 4.2 6.2 - - - +
1394I GLY* 1.3 77.1 + - - -
1396I LEU* 1.3 63.4 + - - +
1397I SER* 3.4 18.0 + - - +
1402I PRO* 4.2 21.3 - - + -
1404I MET 3.7 7.2 - - - +
1405I GLU* 3.8 18.5 + - + +
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Residues in contact with LEU1396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326I ALA* 3.5 42.4 - - + +
1329I VAL* 4.3 10.5 - - + -
1330I GLY* 4.7 2.5 - - - -
1334I ILE* 6.3 0.2 - - + -
1366I LEU* 4.5 9.0 - - + -
1372I VAL* 3.8 20.2 - - + -
1373I SER 3.4 4.9 - - - -
1374I THR* 3.4 27.1 - - + -
1394I GLY* 4.7 1.8 - - - -
1395I THR* 1.3 74.9 - - - +
1397I SER* 1.3 52.7 + - - +
1402I PRO* 3.8 0.3 - - - +
1403I VAL* 2.7 33.3 + - + +
1404I MET* 3.0 29.4 + - + +
1406I VAL* 4.3 19.3 - - + -
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Residues in contact with SER1397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372I VAL* 3.4 8.8 - - - +
1373I SER* 2.8 42.2 + - - -
1375I THR* 5.6 1.6 + - - -
1395I THR* 3.5 18.4 + - - +
1396I LEU* 1.3 76.2 - - - +
1398I ARG* 1.3 61.1 + - - +
1400I GLY 4.3 9.2 - - - -
1401I LYS 3.3 16.4 - - - -
1402I PRO* 3.9 7.6 - - - +
1403I VAL* 4.5 0.7 - - - -
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Residues in contact with ARG1398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363I ALA* 5.0 0.6 - - - +
1364I LYS* 3.1 33.3 + - - +
1365I PRO 2.8 32.3 + - - -
1366I LEU* 3.7 10.4 - - + +
1370I ASP* 2.8 31.8 + - + +
1371I VAL 4.0 16.2 - - - +
1372I VAL* 5.2 5.8 - - + -
1373I SER* 5.7 0.9 - - - -
1397I SER* 1.3 75.5 - - - +
1399I ASN* 1.3 91.8 + - - +
1400I GLY 3.3 0.7 - - - -
1401I LYS* 2.8 23.6 + - - +
1403I VAL* 3.3 27.9 - - + +
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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