Contacts of the strand formed by residues 1418 - 1428 (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 GLU1418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A PRO* 3.6 36.5 - - + +
569A ASP* 5.8 1.1 - - - +
572A GLN* 5.6 5.8 - - + -
1408A SER 3.8 0.5 - - - +
1409A VAL* 3.5 3.8 - - - -
1410A LYS* 3.1 36.1 + - + +
1415A ALA 4.3 5.9 + - - +
1416A LYS* 3.7 2.0 - - - +
1417A GLU* 1.3 74.6 - - - +
1419A HIS* 1.3 59.2 + - - +
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Residues in contact with HIS1419 (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* 4.9 6.0 - - - +
571A ILE* 5.1 7.8 - - - +
1355A TYR* 3.0 27.5 + + - +
1375A ARG* 3.9 12.5 + - - -
1407A CYS* 5.5 0.4 - - + -
1408A SER 3.4 4.5 - - - +
1409A VAL* 3.4 29.2 - - + +
1417A GLU* 3.0 39.2 + - - +
1418A GLU* 1.3 75.0 - - - +
1420A CYS* 1.3 63.1 + - - +
1421A PRO* 4.8 0.3 - - - +
1453A GLU 5.5 1.6 - - - +
1455A LEU* 3.8 27.3 - - + +
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Residues in contact with CYS1420 (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* 3.9 22.4 - - - -
567A LYS* 4.4 16.8 - - + -
568A PRO* 3.9 19.7 - - + +
571A ILE* 5.7 3.1 - - + -
1407A CYS* 3.2 7.0 - - - -
1408A SER* 3.0 49.4 + - - -
1419A HIS* 1.3 76.9 - - - +
1421A PRO* 1.3 69.3 - - + +
1422A LEU* 3.4 15.3 + - - -
1455A LEU* 4.3 2.2 - - - -
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Residues in contact with PRO1421 (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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567A LYS* 5.6 10.7 - - + +
571A ILE* 6.3 1.6 - - + -
1405A SER* 4.9 4.5 - - - +
1406A ILE 3.4 6.1 - - - +
1407A CYS* 4.2 4.9 - - - -
1420A CYS* 1.3 87.4 - - + +
1422A LEU* 1.3 64.4 + - - +
1423A ALA 3.3 3.4 - - - +
1424A TRP* 6.1 1.6 - - + -
1448A VAL* 2.9 36.6 - - + +
1452A LEU 4.5 5.6 - - - +
1453A GLU* 4.5 7.9 - - - +
1454A ASP 3.3 26.2 - - - +
1455A LEU* 4.0 23.3 - - + +
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Residues in contact with LEU1422 (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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560A ASP* 5.7 1.2 - - - +
564A ASN* 3.3 44.1 + - + +
1344A VAL* 4.3 13.7 - - + -
1345A ASN 5.4 0.4 - - - +
1346A VAL* 3.3 29.6 - - + -
1354A ILE* 4.2 15.3 - - + -
1406A ILE* 2.7 36.1 + - + +
1407A CYS 4.4 0.7 - - - -
1408A SER* 4.2 18.2 - - - +
1420A CYS* 3.4 9.0 + - - -
1421A PRO* 1.3 73.4 - - - +
1423A ALA* 1.3 61.9 + - + +
1446A TRP 4.8 0.2 - - - +
1447A PRO* 5.1 2.3 - - - +
1448A VAL* 3.6 10.7 + - - +
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Residues in contact with ALA1423 (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* 6.4 0.9 - - + -
1405A SER* 3.0 6.8 - - - -
1406A ILE* 2.8 30.6 + - + +
1421A PRO* 3.3 3.0 - - - -
1422A LEU* 1.3 83.3 - - + +
1424A TRP* 1.3 61.8 + - - +
1445A LEU* 3.9 24.5 - - + -
1446A TRP 3.7 15.0 - - - +
1447A PRO* 5.5 0.2 - - + -
1448A VAL* 4.4 2.9 - - - -
1471A PRO* 4.3 16.8 - - + -
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Residues in contact with TRP1424 (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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1404A LEU 3.5 11.0 - - - +
1405A SER* 4.0 8.3 - - - +
1421A PRO* 6.1 2.0 - - + -
1423A ALA* 1.3 77.7 - - - +
1425A GLY* 1.3 83.3 + - - +
1426A ASN* 3.8 11.9 - - - -
1445A LEU* 3.2 9.8 - - - +
1446A TRP* 2.8 69.5 + + + +
1447A PRO 2.8 26.4 + - - -
1448A VAL* 3.9 14.1 - - + -
1449A PRO* 3.8 12.3 - - + +
1452A LEU* 6.2 0.2 - - + -
1456A LEU* 5.7 0.4 - - - -
1457A ASN* 3.4 45.5 - - + +
1460A GLY* 3.7 18.4 - - - -
1461A VAL* 3.7 27.1 - - + -
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Residues in contact with GLY1425 (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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1404A LEU* 3.0 30.3 + - - +
1424A TRP* 1.3 87.1 - - - +
1426A ASN* 1.3 72.0 + - - +
1443A LEU* 4.2 9.9 - - - -
1445A LEU* 4.1 12.4 - - - +
1446A TRP* 4.5 7.0 - - - -
1463A GLY 5.5 1.1 - - - -
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Residues in contact with ASN1426 (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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1401A ARG* 3.2 24.2 - - - +
1402A LEU 3.3 4.9 - - - +
1403A CYS* 3.3 21.8 - - - +
1404A LEU* 4.1 0.7 + - - +
1424A TRP* 3.8 8.6 - - - -
1425A GLY* 1.3 84.5 - - - +
1427A ILE* 1.3 69.6 + - - +
1443A LEU* 4.4 2.2 - - - +
1457A ASN 2.9 27.6 + - - +
1458A PRO* 3.7 1.4 + - - +
1460A GLY 3.1 23.4 + - - -
1461A VAL 3.9 12.7 + - - +
1462A THR* 3.9 3.6 - - + -
1463A GLY* 2.9 28.6 + - - +
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Residues in contact with ILE1427 (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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1401A ARG* 3.2 6.2 - - - +
1402A LEU* 2.8 47.1 + - + +
1404A LEU* 5.2 1.6 - - + -
1426A ASN* 1.3 82.1 - - - +
1428A ASN* 1.3 78.7 + - - +
1429A LEU* 4.4 2.7 - - + +
1437A VAL* 4.5 10.8 - - + -
1441A MET* 3.4 33.4 - - + -
1443A LEU* 3.8 30.3 - - + -
1462A THR* 4.1 6.3 - - - -
1463A GLY* 4.7 2.9 - - - +
1475A LEU* 3.9 18.4 - - + -
1477A PHE* 4.8 5.4 - - + -
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Residues in contact with ASN1428 (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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1400A ALA 4.3 4.3 - - - +
1401A ARG* 3.4 22.4 - - - +
1427A ILE* 1.3 83.3 - - - +
1429A LEU* 1.3 63.8 + - - +
1430A PHE 3.3 21.9 + - - +
1431A ASP* 4.6 2.3 + - - -
1437A VAL* 3.4 8.5 - - - +
1462A THR* 3.4 28.6 + - - +
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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