Contacts of the strand formed by residues 1353 - 1362 (chain A) in PDB entry 4YKN
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 LYS1353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1352A ASP* 1.3 91.6 + - + +
1354A ILE* 1.3 66.9 + - - +
1375A ARG* 3.9 34.9 + - + +
1376A VAL* 3.5 19.9 - - - +
1377A PRO* 4.0 21.3 - - + +
1378A CYS* 4.4 0.6 - - - -
1408A SER* 3.3 5.2 - - - -
1409A VAL* 2.9 34.8 + - + -
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Residues in contact with ILE1354 (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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1344A VAL* 4.1 15.0 - - + -
1346A VAL* 4.8 3.4 - - + -
1353A LYS* 1.3 81.0 - - - +
1355A TYR* 1.3 66.9 + - - +
1374A GLN 4.1 0.7 - - - +
1375A ARG* 3.5 1.8 - - - -
1376A VAL* 3.0 39.7 + - + +
1377A PRO 4.3 3.1 - - - +
1378A CYS* 3.6 34.3 - - + +
1381A PRO* 3.9 27.6 - - + -
1383A TRP* 4.2 13.7 - - + -
1406A ILE* 4.6 8.5 - - + -
1407A CYS 3.1 14.1 - - - +
1408A SER* 4.1 11.7 - - - +
1422A LEU* 4.2 11.0 - - + -
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Residues in contact with TYR1355 (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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1354A ILE* 1.3 78.8 - - - +
1356A VAL* 1.3 71.7 + - - +
1357A ARG* 3.8 14.1 + - + -
1372A ASN* 3.6 39.2 + - + -
1373A THR* 3.8 15.7 - - - +
1374A GLN 4.0 8.1 - - - +
1375A ARG* 4.3 14.6 - - + -
1383A TRP* 3.9 7.9 - - - +
1406A ILE* 3.4 4.1 - - - +
1407A CYS* 2.8 57.9 + - + +
1409A VAL* 3.6 29.8 - - + -
1419A HIS* 3.0 25.6 + + - -
1455A LEU* 4.0 14.6 - - - +
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Residues in contact with VAL1356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1338A ILE* 3.8 23.8 - - + -
1355A TYR* 1.3 72.9 - - - +
1357A ARG* 1.3 62.3 + - - +
1358A THR* 3.9 21.1 + - + +
1371A VAL 4.2 0.3 - - - +
1372A ASN* 3.6 2.3 - - - -
1373A THR* 2.9 42.1 + - + +
1383A TRP* 3.6 34.3 - - + -
1404A LEU* 4.6 2.9 - - + -
1405A SER 3.3 11.2 - - - +
1406A ILE* 4.2 8.7 - - + -
1473A LEU* 4.0 22.2 - - + -
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Residues in contact with ARG1357 (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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349A ASP* 3.0 34.0 + - - +
373A ARG* 5.7 0.4 - - - +
1355A TYR* 3.8 17.3 + - + -
1356A VAL* 1.3 71.7 - - - +
1358A THR* 1.3 61.8 + - - +
1369A ASP* 5.5 2.2 + - - -
1370A ASN* 2.9 36.6 + - - +
1372A ASN* 3.0 47.4 + - - +
1404A LEU* 3.1 4.7 - - - +
1405A SER* 2.8 47.9 + - - +
1407A CYS* 3.9 4.7 - - - -
1455A LEU* 3.6 36.8 - - - +
1456A LEU* 3.5 18.2 - - + +
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Residues in contact with THR1358 (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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1338A ILE* 4.1 8.3 - - + -
1356A VAL* 3.9 17.5 - - + +
1357A ARG* 1.3 79.2 - - - +
1359A GLY* 1.3 58.5 + - - +
1370A ASN* 3.3 12.1 - - - +
1371A VAL 2.8 38.9 + - - +
1387A LEU* 3.5 22.6 - - + +
1389A TYR* 2.7 31.6 + - - +
1402A LEU* 4.4 4.5 - - + -
1403A CYS 3.4 8.7 - - - -
1404A LEU* 4.0 11.7 - - + +
1456A LEU* 4.2 4.7 - - - +
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Residues in contact with GLY1359 (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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1358A THR* 1.3 79.2 - - - +
1360A ILE* 1.3 65.4 + - - -
1361A TYR* 3.7 8.5 - - - -
1369A ASP 5.4 0.7 - - - -
1370A ASN* 3.6 21.1 - - - -
1389A TYR* 4.5 5.6 - - - -
1402A LEU* 3.5 4.5 - - - +
1403A CYS* 2.8 34.8 + - - +
1456A LEU* 4.3 0.2 - - - +
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Residues in contact with ILE1360 (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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1334A LEU* 3.8 26.9 - - + -
1336A ILE* 4.4 3.6 - - + -
1359A GLY* 1.3 72.1 - - - -
1361A TYR* 1.3 62.9 + - - +
1366A PRO* 3.5 5.5 - - - +
1367A LEU* 2.9 43.9 + - + -
1368A CYS* 4.3 18.9 + - - +
1370A ASN* 4.9 0.6 - - - +
1389A TYR* 3.9 23.6 - - + -
1391A ILE* 5.2 2.2 - - + -
1396A LEU* 4.2 10.3 - - + -
1400A ALA* 4.4 2.2 - - + -
1401A ARG 3.6 3.6 - - - +
1402A LEU* 3.6 26.0 - - + -
1429A LEU* 3.9 27.8 - - + -
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Residues in contact with TYR1361 (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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1359A GLY 3.7 12.3 - - - -
1360A ILE* 1.3 79.4 - - - +
1362A HIS* 1.3 58.5 + - - +
1363A GLY 3.9 10.6 + - - +
1364A GLY 3.5 22.4 - - - -
1365A GLU 3.4 3.1 - - - -
1366A PRO* 3.5 35.1 - - + +
1367A LEU* 4.3 3.4 - - - -
1370A ASN* 3.4 34.1 + - - -
1399A ALA 4.4 0.3 - - - +
1400A ALA* 3.5 2.8 - - - -
1401A ARG* 2.9 37.1 + - - +
1403A CYS* 3.9 26.2 - - + -
1456A LEU* 3.7 23.1 - - + +
1458A PRO* 3.9 19.2 - - + +
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Residues in contact with HIS1362 (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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1361A TYR* 1.3 71.8 - - - +
1363A GLY* 1.3 66.6 + - - +
1364A GLY 3.5 0.2 + - - -
1365A GLU* 2.8 36.6 + - - +
1367A LEU* 3.6 28.6 - - + +
1397A PRO* 3.8 28.6 - - + +
1399A ALA* 4.0 29.2 + - + +
1400A ALA* 4.8 0.9 - - - +
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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