Contacts of the strand formed by residues 1401 - 1410 (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 ARG1401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360A ILE* 3.6 3.3 - - - +
1361A TYR* 2.9 38.5 + - - +
1363A GLY* 3.4 25.3 + - - +
1399A ALA 3.5 16.0 + - - +
1400A ALA* 1.3 74.3 - - - +
1402A LEU* 1.3 61.9 + - - +
1403A CYS* 3.8 5.8 + - - -
1426A ASN* 3.2 37.8 - - - +
1427A ILE 3.2 9.6 - - - +
1428A ASN* 3.4 26.9 - - - +
1429A LEU* 4.2 5.6 - - - -
1458A PRO* 2.5 34.2 + - - +
1460A GLY 3.8 4.2 + - - -
1462A THR* 3.7 12.3 - - - +
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Residues in contact with LEU1402 (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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1336A ILE* 3.8 25.8 - - + -
1358A THR* 4.4 4.9 - - + -
1359A GLY 3.5 19.3 - - - +
1360A ILE* 3.6 17.9 - - + -
1389A TYR* 4.2 10.5 - - - +
1401A ARG* 1.3 70.3 - - - +
1403A CYS* 1.3 65.4 + - - +
1404A LEU* 3.8 26.5 + - + +
1425A GLY 4.2 0.3 - - - +
1426A ASN* 3.3 5.2 - - - +
1427A ILE* 2.8 45.0 + - + +
1429A LEU* 3.9 18.3 - - + +
1475A LEU* 4.3 13.9 - - + -
1477A PHE* 4.3 9.0 - - + -
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Residues in contact with CYS1403 (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* 3.4 1.9 - - - -
1359A GLY 2.8 39.2 + - - +
1361A TYR* 3.9 28.3 - - + -
1401A ARG* 3.8 16.8 - - - -
1402A LEU* 1.3 76.0 - - - +
1404A LEU* 1.3 60.2 + - - +
1426A ASN* 3.3 25.6 - - - +
1456A LEU* 3.9 12.9 - - + +
1457A ASN 5.1 0.4 - - - +
1458A PRO* 3.8 28.5 - - + -
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Residues in contact with LEU1404 (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* 4.9 1.3 - - + -
1356A VAL* 4.6 2.5 - - + -
1357A ARG 3.1 11.7 - - - +
1358A THR* 4.0 16.4 - - + -
1402A LEU* 3.8 30.1 - - + +
1403A CYS* 1.3 74.9 - - - +
1405A SER* 1.3 66.7 + - - +
1424A TRP* 3.5 1.9 - - - +
1425A GLY 3.0 38.6 + - - +
1426A ASN* 4.1 0.8 + - - +
1427A ILE* 5.2 1.1 - - + -
1443A LEU* 3.9 17.7 - - + -
1445A LEU* 4.1 9.6 - - + -
1456A LEU* 3.8 3.8 - - - +
1457A ASN 5.9 0.3 + - - -
1473A LEU* 3.7 26.9 - - + -
1475A LEU* 3.9 22.9 - - + -
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Residues in contact with SER1405 (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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1356A VAL* 3.3 7.4 - - - +
1357A ARG* 2.8 33.2 + - - +
1404A LEU* 1.3 80.2 - - - +
1406A ILE* 1.3 60.3 + - - +
1407A CYS* 3.3 13.6 - - - -
1421A PRO* 5.0 3.4 - - - -
1423A ALA 3.0 18.2 - - - -
1424A TRP* 4.0 9.9 - - - +
1445A LEU* 5.5 0.4 - - - -
1455A LEU 2.7 29.2 + - - -
1456A LEU* 3.4 8.1 - - - +
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Residues in contact with ILE1406 (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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1341A ALA* 3.9 21.8 - - + -
1344A VAL* 3.9 25.8 - - + -
1354A ILE* 4.6 11.2 - - + -
1355A TYR 3.4 10.3 - - - +
1356A VAL* 4.2 14.4 - - + -
1383A TRP* 5.0 3.4 - - + -
1405A SER* 1.3 76.3 - - - +
1407A CYS* 1.3 57.9 + - - +
1421A PRO* 3.4 2.3 - - - +
1422A LEU* 2.7 55.5 + - + +
1423A ALA* 2.8 16.0 + - + +
1445A LEU* 3.9 24.9 - - + -
1471A PRO* 5.1 3.6 - - + -
1473A LEU* 4.7 7.9 - - + -
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Residues in contact with CYS1407 (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* 3.1 6.9 - - - +
1355A TYR* 2.8 59.2 + - + +
1357A ARG* 3.9 18.4 - - - -
1405A SER* 3.3 24.0 - - - -
1406A ILE* 1.3 74.8 - - - +
1408A SER* 1.3 61.9 + - - +
1419A HIS* 5.2 0.2 - - - +
1420A CYS 3.2 11.7 - - - +
1421A PRO* 4.2 8.3 - - - -
1422A LEU* 4.2 4.0 - - - +
1455A LEU* 4.0 19.5 - - + -
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Residues in contact with SER1408 (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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564A ASN* 5.0 2.1 + - - +
568A PRO* 5.1 3.3 - - - +
1346A VAL* 4.8 0.9 - - - -
1351A ILE* 4.3 18.8 - - - +
1353A LYS 3.3 11.2 - - - -
1354A ILE* 4.1 11.2 - - - +
1407A CYS* 1.3 75.0 - - - +
1409A VAL* 1.3 66.9 + - - +
1410A LYS* 4.9 1.0 + - - +
1418A GLU 3.8 0.7 - - - +
1419A HIS* 3.4 7.4 + - - +
1420A CYS* 3.0 45.1 + - - -
1422A LEU* 4.2 15.6 - - - +
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Residues in contact with VAL1409 (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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1351A ILE* 5.0 0.7 - - - -
1352A ASP* 3.2 23.9 + - - +
1353A LYS* 2.9 22.1 + - + +
1355A TYR* 3.6 17.3 - - + -
1375A ARG* 3.8 30.7 - - - +
1408A SER* 1.3 76.9 - - - +
1410A LYS* 1.3 66.4 + - - +
1411A GLY* 5.5 0.9 - - - -
1417A GLU* 3.9 27.8 - - + +
1418A GLU 3.5 4.9 - - - +
1419A HIS* 3.4 32.1 - - + +
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Residues in contact with LYS1410 (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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568A PRO* 4.7 14.5 - - + +
569A ASP* 5.7 4.0 - - - +
1351A ILE* 4.7 9.2 - - + +
1352A ASP* 4.4 6.3 - - - +
1408A SER* 4.2 2.4 + - - +
1409A VAL* 1.3 74.0 - - - +
1411A GLY* 1.3 67.3 + - - +
1415A ALA* 5.0 0.3 - - - +
1417A GLU* 3.7 22.0 - - - -
1418A GLU* 3.1 24.4 + - + +
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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