Contacts of the strand formed by residues 1344 - 1350 (chain E) in PDB entry 6C3P
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 ILE1344 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1342E GLY* 3.3 17.7 - - - +
1343E LYS* 1.3 75.9 - - - +
1345E GLN* 1.3 59.6 + - - +
1346E ILE* 4.0 9.4 - - + -
1366E ALA 3.2 3.0 - - - +
1368E ILE* 2.3 68.6 + - + +
1391E PHE* 4.8 22.4 - - + -
1402E ILE* 3.7 31.6 - - + -
1403E ILE 3.5 5.2 - - - +
1404E ILE* 4.9 14.8 - - + -
1501E ILE* 5.5 13.0 - - + -
1531E THR* 5.6 3.4 - - + -
1533E VAL* 5.3 7.2 - - + -
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Residues in contact with GLN1345 (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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1343E LYS* 4.3 4.7 - - - -
1344E ILE* 1.3 73.1 - - - +
1346E ILE* 1.3 64.0 + - - +
1347E GLN* 5.5 1.4 - - - +
1366E ALA 3.0 7.2 - - - +
1367E LEU* 4.1 22.0 - - + -
1401E HIS* 4.5 1.2 + - - +
1402E ILE* 4.0 0.5 - - - -
1403E ILE* 3.1 42.6 + - + +
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Residues in contact with ILE1346 (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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1344E ILE* 4.0 9.0 - - + -
1345E GLN* 1.3 76.2 - - - +
1347E GLN* 1.3 64.3 + - - +
1349E LEU* 4.1 11.9 - - + -
1364E VAL* 3.5 38.1 - - + +
1365E ASN* 3.1 3.6 - - - +
1366E ALA* 2.7 55.8 + - + +
1368E ILE* 5.8 1.6 - - + -
1387E PHE* 3.5 30.3 - - + -
1401E HIS 3.9 7.0 - - - +
1402E ILE* 3.6 32.8 - - + +
1556E ILE* 5.4 0.2 - - + -
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Residues in contact with GLN1347 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1345E GLN 5.5 0.9 - - - +
1346E ILE* 1.3 78.9 - - - +
1348E ASN* 1.3 75.0 + - + +
1349E LEU 2.9 5.6 + - - +
1364E VAL 3.2 4.6 + - - -
1365E ASN* 3.6 11.7 - - + +
1400E GLY* 3.8 1.0 - - - -
1401E HIS* 2.9 57.8 + - + +
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Residues in contact with ASN1348 (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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1347E GLN* 1.3 77.2 - - + +
1349E LEU* 1.3 63.9 + - - +
1350E SER* 3.0 14.3 + - - -
1363E HIS* 3.9 26.6 - - + +
1364E VAL 2.9 17.6 + - - +
1365E ASN* 4.3 2.4 - - - +
1399E GLU* 4.4 1.3 - - + +
1400E GLY* 3.2 17.0 + - - +
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Residues in contact with LEU1349 (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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1346E ILE* 4.1 18.6 - - + -
1347E GLN 2.9 7.0 + - - +
1348E ASN* 1.3 72.3 - - - +
1350E SER* 1.3 58.2 + - - +
1351E VAL* 4.1 13.2 - - + -
1361E LEU* 3.3 10.9 - - + +
1362E LYS* 3.4 5.5 - - - -
1363E HIS 3.5 0.2 + - - -
1364E VAL* 3.1 31.9 + - + +
1387E PHE* 3.6 35.4 - - + -
1390E ALA* 4.2 14.4 - - + +
1397E THR* 3.8 23.1 - - - +
1400E GLY* 4.1 2.9 - - - -
1401E HIS* 4.2 22.4 - - - +
1402E ILE* 4.5 11.0 - - + +
1409E ILE* 6.5 0.2 - - + -
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Residues in contact with SER1350 (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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1348E ASN 3.0 12.8 + - - -
1349E LEU* 1.3 70.5 - - - +
1351E VAL* 1.3 62.3 + - - +
1361E LEU 3.1 4.3 - - - -
1362E LYS* 3.4 20.9 - - - +
1363E HIS* 3.4 12.1 + - - -
1397E THR 3.2 1.2 - - - -
1398E PHE* 3.0 39.5 + - - -
1399E GLU* 3.1 35.1 + - - +
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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