Contacts of the strand formed by residues 1350 - 1358 (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 HIS1350 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1344E VAL* 3.6 7.3 - - - +
1345E SER* 3.2 23.8 + - - -
1349E ILE* 1.3 82.6 - - + +
1351E ALA* 1.3 64.7 + - - +
1401E SER* 3.6 27.5 + - - -
1402E LEU 3.2 5.0 + - - +
1403E LYS* 3.6 24.0 - - + +
1404E VAL* 4.9 1.6 - - - -
1642F LEU* 3.8 14.8 - - + +
1643F ASN* 2.8 43.9 + - - -
1652F ASP* 3.0 32.0 + - + +
1700F TYR* 3.7 23.7 - + + +
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Residues in contact with ALA1351 (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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1341E LEU* 4.4 11.9 - - + -
1343E ASN 3.5 11.4 - - - +
1344E VAL* 4.6 9.6 - - + -
1350E HIS* 1.3 78.5 - - - +
1352E ASP* 1.3 67.9 + - - +
1353E ILE* 4.9 0.4 - - - -
1401E SER 3.5 0.7 + - - -
1402E LEU* 2.7 47.4 + - - +
1404E VAL* 4.8 4.5 - - + -
1433E LEU* 4.2 25.1 - - + -
1434E PRO* 5.8 0.7 - - + -
1700F TYR* 4.5 0.4 - - - -
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Residues in contact with ASP1352 (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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1341E LEU* 3.3 8.7 - - - +
1342E LEU* 2.8 42.9 + - + +
1343E ASN* 3.1 19.2 + - - +
1351E ALA* 1.3 72.6 - - - +
1353E ILE* 1.3 63.3 + - - +
1399E VAL 3.5 6.7 - - - +
1400E TYR* 3.1 30.7 - - + -
1401E SER 3.3 4.0 + - - -
1698F PRO* 4.0 9.0 - - - +
1700F TYR* 2.7 37.5 + - - -
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Residues in contact with ILE1353 (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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1339E TRP* 3.6 25.8 - - + -
1340E THR 3.1 11.7 - - - +
1341E LEU* 3.9 2.0 - - + -
1342E LEU* 3.9 4.9 - - - -
1351E ALA 4.9 0.2 - - - -
1352E ASP* 1.3 80.9 - - - +
1354E GLN* 1.3 58.2 + - - +
1355E VAL* 3.9 22.2 - - + -
1398E PRO* 3.4 2.3 - - - +
1399E VAL* 2.7 49.1 + - + +
1402E LEU* 3.7 27.8 - - + -
1410E VAL* 5.3 3.4 - - + -
1431E VAL* 4.0 17.9 - - + -
1433E LEU* 3.6 29.8 - - + -
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Residues in contact with GLN1354 (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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1338E ASN 4.0 0.2 - - - +
1339E TRP* 3.4 2.8 - - - -
1340E THR* 2.8 40.5 + - + +
1342E LEU* 3.8 24.0 - - + +
1353E ILE* 1.3 72.5 - - - +
1355E VAL* 1.3 59.4 + - - +
1356E ARG* 3.8 13.0 + - + +
1396E SER* 2.5 31.8 + - - +
1397E VAL* 2.8 29.0 - - - +
1398E PRO* 3.6 17.8 - - - +
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Residues in contact with VAL1355 (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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1337E LEU* 4.0 14.8 - - + -
1338E ASN 4.0 2.0 - - - -
1339E TRP* 4.4 6.3 - - + -
1353E ILE* 3.9 21.2 + - + -
1354E GLN* 1.3 73.1 - - - +
1356E ARG* 1.3 68.3 + - - +
1357E TRP* 3.4 20.4 - - + -
1376E LEU* 3.7 22.4 - - + -
1396E SER* 3.3 2.8 + - - -
1397E VAL 2.6 42.2 + - - +
1399E VAL* 3.8 20.0 - - + -
1410E VAL* 4.3 14.1 - - + -
1429E LEU* 4.6 6.1 - - + -
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Residues in contact with ARG1356 (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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1336E ALA 4.4 0.7 - - - -
1337E LEU* 3.6 1.2 - - - -
1338E ASN* 3.0 45.6 + - + +
1340E THR* 4.8 13.9 + - - -
1354E GLN* 4.3 11.2 - - + +
1355E VAL* 1.3 75.7 - - - +
1357E TRP* 1.3 71.8 + - - +
1395E THR 3.6 6.7 - - - +
1396E SER* 3.1 24.9 - - - +
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Residues in contact with TRP1357 (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* 3.7 11.9 - - + -
1335E ILE 3.5 3.8 - - - +
1336E ALA* 3.7 7.2 - - - -
1337E LEU* 3.2 26.2 - - + -
1355E VAL* 3.4 34.8 - - + -
1356E ARG* 1.3 91.9 - - - +
1358E GLU* 1.3 73.8 + - - +
1374E TYR* 3.6 29.7 - + + -
1376E LEU* 4.0 14.1 - - + -
1392E ILE* 3.4 34.5 - - + -
1394E THR 3.5 5.4 - - - -
1395E THR* 3.0 42.4 + - - +
1396E SER* 4.0 6.5 - - - -
1397E VAL* 3.8 18.8 - - + -
1412E VAL* 4.1 13.7 - - + +
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Residues in contact with GLU1358 (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* 3.2 11.4 - - - +
1335E ILE* 2.9 52.3 + - + +
1336E ALA* 4.0 13.6 - - + +
1357E TRP* 1.3 77.4 - - - +
1359E ALA* 1.3 80.9 - - + +
1361E ARG* 2.7 37.6 + - - -
1395E THR* 4.9 1.8 - - - -
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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