Contacts of the strand formed by residues 1486 - 1493 (chain B) in PDB entry 1KI1
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 PHE1486 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1449B LEU* 3.6 33.9 - - + -
1451B PHE* 4.2 6.1 - + - -
1461B ARG* 3.4 24.0 - - - -
1483B PHE* 2.9 53.8 + + - -
1485B ASP* 1.3 105.9 + - - +
1487B LEU* 1.3 64.5 + - - +
1488B LEU* 3.9 10.8 - - + -
1518B PRO* 3.6 23.8 - - + -
1519B ILE 3.4 14.6 - - - +
1520B PHE* 3.8 24.9 - + + -
1521B LEU* 3.4 10.5 - - - +
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Residues in contact with LEU1487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1469B LEU* 6.4 1.1 - - + -
1480B GLY 4.9 0.7 - - - -
1481B PHE 3.5 18.8 - - - +
1482B LEU* 4.0 16.2 - - + -
1486B PHE* 1.3 73.0 - - - +
1488B LEU* 1.3 67.3 + - - +
1489B LEU* 4.1 17.9 + - + -
1518B PRO* 3.8 2.3 - - - +
1519B ILE* 2.8 53.5 + - + +
1521B LEU* 3.5 5.5 - - + +
1539B PHE* 6.1 0.4 - - + -
1541B ILE* 3.8 28.0 - - + -
1550B LEU* 5.2 7.9 - - + -
1561B TRP* 3.9 27.4 - - + -
1565B ILE* 4.4 12.8 - - + -
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Residues in contact with LEU1488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440B VAL* 3.7 18.8 - - + -
1442B CYS* 5.1 0.2 - - - -
1449B LEU* 5.2 0.7 - - + -
1451B PHE* 4.1 19.5 - - + -
1479B TYR 4.1 0.2 - - - +
1480B GLY* 3.0 5.7 - - - -
1481B PHE* 2.7 58.2 + - + +
1483B PHE* 4.1 4.3 - - + -
1486B PHE* 3.9 19.9 + - + -
1487B LEU* 1.3 73.5 - - - +
1489B LEU* 1.3 64.8 + - - +
1490B THR* 3.6 20.2 - - + -
1514B MET* 3.6 42.4 - - + -
1518B PRO* 4.5 7.6 - - + -
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Residues in contact with LEU1489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1468B LYS 5.9 0.4 - - - +
1469B LEU* 5.6 7.4 - - + +
1478B LEU* 5.0 15.5 - - + -
1479B TYR 4.0 1.1 - - - +
1480B GLY* 4.4 11.9 - - - +
1487B LEU* 4.1 22.6 + - + +
1488B LEU* 1.3 78.9 - - - +
1490B THR* 1.3 61.0 + - - +
1514B MET* 3.5 4.0 - - - +
1515B TYR* 2.6 60.8 + - + +
1516B LYS* 5.1 3.3 - - + +
1518B PRO* 5.9 0.6 - - - +
1519B ILE* 5.4 6.5 - - + -
1548B TYR* 4.7 25.8 - - + -
1550B LEU* 4.7 19.7 - - + -
1561B TRP* 6.5 0.2 - - + -
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Residues in contact with THR1490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440B VAL* 3.8 11.9 - - + -
1478B LEU* 3.2 16.2 - - - +
1479B TYR* 2.6 49.2 + - - +
1481B PHE* 3.5 14.7 - - + -
1488B LEU* 3.6 28.9 - - + -
1489B LEU* 1.3 80.4 - - - +
1491B GLN* 1.3 61.9 + - - +
1512B GLN* 3.9 11.4 - - - +
1513B TYR 3.0 12.1 - - - -
1514B MET* 3.7 12.1 - - - -
1515B TYR* 4.0 2.5 - - - +
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Residues in contact with GLN1491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477B GLU* 3.6 34.3 + - + +
1478B LEU* 4.6 6.9 - - + +
1479B TYR 4.7 0.2 - - - +
1490B THR* 1.3 77.2 - - - +
1492B ILE* 1.3 69.5 + - - +
1493B THR* 3.0 18.3 + - - +
1512B GLN* 3.2 4.9 - - - -
1513B TYR* 2.7 41.4 + - + +
1515B TYR* 6.5 0.2 - - - -
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Residues in contact with ILE1492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1468B LYS* 1.7 53.6 - - + +
1477B GLU* 5.0 8.7 + - + +
1478B LEU 5.5 3.8 - - - +
1479B TYR* 4.0 15.5 - - + +
1491B GLN* 1.3 75.1 + - - +
1493B THR* 1.3 63.8 + - - +
1494B LYS* 3.4 14.0 + - + +
1510B ASN* 4.4 20.6 - - - +
1512B GLN* 4.1 11.7 - - + +
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Residues in contact with THR1493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441B GLN* 5.4 1.6 + - - -
1491B GLN* 3.0 18.4 + - - +
1492B ILE* 1.3 71.8 - - - +
1494B LYS* 1.3 67.6 + - - +
1495B PRO* 4.5 1.7 - - - +
1510B ASN* 4.3 7.3 + - - -
1511B LEU* 3.1 33.4 + - + +
1513B TYR* 4.0 17.5 + - - +
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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