Contacts of the strand formed by residues 1372 - 1380 (chain E) in PDB entry 1KF9
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 LEU1372 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1331E PRO* 4.3 9.0 - - + -
1359E ALA* 4.8 0.2 - - + -
1360E PRO* 3.7 27.4 - - + -
1363E ALA* 3.7 28.0 - - + -
1365E ILE* 4.1 14.7 - - + +
1370E MET* 3.9 20.3 + - + -
1371E VAL* 1.3 82.0 - - - +
1373E GLU* 1.3 57.5 + - - +
1374E TYR* 3.7 22.5 - - + +
1393E LEU* 3.8 25.1 - - - +
1414E SER* 3.8 13.2 - - - +
1415E LYS 3.5 15.0 - - - +
1416E GLN* 3.9 9.4 - - - +
1417E ARG* 5.0 0.2 - - - -
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Residues in contact with GLU1373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371E VAL 4.0 0.2 + - - -
1372E LEU* 1.3 73.2 - - - +
1374E TYR* 1.3 66.3 + - - +
1391E PRO* 3.3 36.2 - - + +
1392E ILE 3.5 9.6 - - - +
1393E LEU* 4.9 6.3 - - + +
1414E SER* 3.7 2.6 - - - -
1415E LYS* 2.9 61.5 + - + +
1417E ARG* 3.4 43.7 + - + -
1418E ASN 4.9 0.7 + - - -
1422E TYR* 3.8 6.2 + - - +
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Residues in contact with TYR1374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334E PRO* 4.4 6.1 - - + -
1357E TRP* 3.6 31.9 - + + -
1359E ALA* 3.5 24.5 - - - +
1360E PRO* 4.5 10.3 - - + -
1365E ILE* 5.3 1.2 - - - +
1372E LEU* 3.7 26.1 + - + +
1373E GLU* 1.3 74.3 - - - +
1375E GLU* 1.3 62.8 + - - +
1390E ASP 4.4 0.3 - - - +
1391E PRO* 3.3 6.9 - - - +
1392E ILE* 2.9 40.8 + - + +
1393E LEU 3.8 12.6 - - - -
1394E THR 3.2 27.1 - - - -
1395E THR* 3.7 11.7 - - + +
1412E VAL* 3.8 11.0 - - + -
1413E ARG 3.3 11.7 - - - +
1414E SER* 3.4 26.5 - - - -
1422E TYR* 4.4 2.5 - - - -
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Residues in contact with GLU1375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374E TYR* 1.3 74.1 - - - +
1376E LEU* 1.3 62.7 + - - +
1377E GLN* 2.7 36.3 + - + +
1388E MET* 3.1 22.4 - - + +
1389E MET 4.0 17.9 - - - +
1390E ASP 5.5 0.4 - - - -
1391E PRO* 4.9 3.1 - - + +
1411E ARG 4.0 0.2 - - - +
1412E VAL* 3.3 3.8 - - - +
1413E ARG* 2.7 50.7 + - + +
1422E TYR* 3.3 38.8 + - + +
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Residues in contact with LEU1376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1355E VAL* 3.7 34.8 - - + -
1357E TRP* 4.0 10.1 - - + -
1374E TYR 4.1 0.8 + - - -
1375E GLU* 1.3 75.1 - - - +
1377E GLN* 1.3 79.9 + - - +
1378E TYR* 3.9 15.5 - - + -
1389E MET* 3.1 53.4 + - + +
1392E ILE* 6.0 2.8 - - + +
1397E VAL* 3.9 21.3 - - + -
1399E VAL* 4.6 2.5 - - + -
1410E VAL* 3.9 8.7 - - + -
1411E ARG 3.3 11.0 - - - +
1412E VAL* 4.0 8.7 - - + -
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Residues in contact with GLN1377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375E GLU* 2.7 28.6 + - + +
1376E LEU* 1.3 83.1 - - - +
1378E TYR* 1.3 59.4 + - - +
1386E TRP* 3.2 26.9 - - + +
1387E LYS 3.2 11.7 - - - +
1388E MET* 3.4 15.2 - - + +
1410E VAL* 3.3 2.8 - - - -
1411E ARG* 2.7 59.4 + - - +
1413E ARG* 3.5 7.9 - - - +
1425E PHE* 3.0 34.2 - - + -
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Residues in contact with TYR1378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376E LEU* 3.9 15.7 - - + -
1377E GLN* 1.3 75.6 - - - +
1379E LYS* 1.3 69.6 + - - +
1386E TRP* 3.8 2.7 - - - -
1387E LYS* 3.0 75.7 + - + +
1388E MET 6.0 0.2 - - - -
1389E MET* 4.6 12.8 - - + -
1399E VAL* 4.0 21.5 - - + +
1400E TYR 4.6 7.3 + - - -
1402E LEU* 3.6 31.9 - - + -
1408E TYR* 4.0 9.0 - + + -
1409E GLU 3.2 7.9 - - - +
1410E VAL* 3.6 22.0 - - + -
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Residues in contact with LYS1379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378E TYR* 1.3 82.2 - - - +
1380E GLU* 1.3 79.1 + - - +
1381E VAL 3.1 6.7 + - - -
1383E GLU* 2.7 36.3 + - + -
1384E THR 4.2 5.6 - - - +
1385E LYS* 3.5 23.8 - - - +
1386E TRP* 3.3 43.5 - - + +
1387E LYS* 4.5 5.2 - - - +
1408E TYR* 3.6 7.8 - - - -
1409E GLU* 3.0 52.5 + - + +
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Residues in contact with GLU1380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379E LYS* 1.3 85.6 - - - +
1381E VAL* 1.3 68.2 + - - +
1382E ASN* 2.8 35.9 + - - +
1383E GLU* 2.6 48.9 + - + +
1387E LYS* 4.8 3.7 - - - +
1406E LYS* 3.0 52.8 + - + +
1407E GLU 3.5 16.9 + - - +
1408E TYR* 3.5 17.4 - - + -
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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