Contacts of the strand formed by residues 1560 - 1565 (chain H) in PDB entry 6X34
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 ASN1560 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1272H LEU 3.6 7.4 - - - +
1273H THR* 5.0 2.5 - - + +
1440H PHE* 3.6 42.7 - - + +
1443H GLN* 3.9 12.0 - - - +
1558H HIS* 3.3 22.9 + - + +
1559H GLN* 1.3 76.7 - - + +
1561H VAL* 1.3 65.9 + - - +
1562H ILE 3.7 0.2 - - - -
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Residues in contact with VAL1561 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272H LEU* 3.3 37.6 + - + -
1274H HIS* 6.2 1.1 - - + -
1289H LEU* 6.0 1.1 - - + -
1439H VAL* 4.7 4.9 - - - +
1440H PHE* 5.0 1.5 + - - -
1443H GLN* 4.3 5.2 - - - +
1554H VAL* 3.4 35.2 - - + +
1555H LEU 4.4 11.4 - - - +
1556H PRO* 4.7 10.8 - - + -
1558H HIS 4.9 2.5 - - - +
1559H GLN 3.6 2.8 + - - +
1560H ASN* 1.3 75.5 - - - +
1562H ILE* 1.3 64.5 + - + +
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Residues in contact with ILE1562 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270H LEU 3.9 1.4 - - - +
1271H ARG* 3.4 1.9 - - - +
1272H LEU* 3.0 27.8 + - + +
1289H LEU* 5.2 7.6 - - + -
1437H VAL* 5.0 5.8 - - + -
1438H ARG 4.3 5.2 - - - +
1439H VAL* 5.2 6.1 - - + +
1440H PHE* 4.4 7.8 - - - -
1448H VAL* 6.5 0.2 - - + -
1552H VAL* 4.3 19.5 - - + -
1554H VAL* 3.8 17.5 - - + -
1560H ASN 3.7 0.6 - - - -
1561H VAL* 1.3 83.5 - - + +
1563H GLN* 1.3 59.8 - - - +
1564H PHE* 5.8 4.0 - - + -
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Residues in contact with GLN1563 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269H CYS* 4.8 6.5 - - + -
1270H LEU 3.6 5.6 - - - -
1271H ARG* 3.8 17.3 - - + +
1437H VAL* 3.3 4.8 - - - +
1438H ARG* 3.0 43.5 + - + +
1440H PHE* 3.6 24.9 - - + -
1562H ILE* 1.3 76.7 - - - +
1564H PHE* 1.3 68.8 + - - +
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Residues in contact with PHE1564 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269H CYS* 3.2 20.7 - - - +
1270H LEU* 3.2 56.4 + - + +
1289H LEU* 5.0 19.1 - - + -
1290H ARG 5.8 0.9 - - - -
1291H LEU* 3.6 33.2 - - + -
1435H TYR* 4.1 17.5 - - + +
1436H SER 4.4 0.7 - - - -
1437H VAL* 4.5 10.5 - - + +
1438H ARG* 4.5 4.5 - - - +
1550H PRO 5.4 0.2 - - - -
1552H VAL* 3.9 30.5 - - + -
1562H ILE* 5.8 3.4 - - + -
1563H GLN* 1.3 80.8 - - - +
1565H GLU* 1.3 65.0 + - - +
1597H MET* 4.7 16.2 - - + -
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Residues in contact with GLU1565 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267H PRO* 5.3 8.5 - - + -
1268H PRO 3.7 7.4 - - - -
1269H CYS* 5.0 0.2 - - - -
1435H TYR* 4.2 13.4 - - - -
1436H SER* 3.0 48.9 + - - +
1437H VAL 4.4 0.2 - - - +
1438H ARG* 4.2 20.6 - - + -
1564H PHE* 1.3 81.7 - - - +
1566H LEU* 1.3 60.7 + - - +
1567H GLY 3.9 1.6 + - - +
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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