Contacts of the strand formed by residues 1033 - 1038 (chain A) in PDB entry 6BM0
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 VAL1033 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027A TYR* 3.6 4.9 - - - -
1028A HIS* 2.8 33.4 + - + +
1031A SER 3.8 2.5 - - - +
1032A LYS* 1.3 80.1 - - - +
1034A TYR* 1.3 66.1 + - - +
1078A LEU* 3.7 21.3 - - + -
1079A ILE 3.6 13.5 - - - +
1080A SER* 4.6 2.2 - - - +
1081A PRO* 3.9 7.6 - - + -
1087A ILE* 4.1 14.4 - - + -
1144A VAL* 3.9 28.7 - - + -
1158A ASN* 3.6 27.6 - - - +
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Residues in contact with TYR1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ALA* 4.8 3.1 - - + -
481A GLY* 3.3 26.7 - - - -
482A GLU 4.1 3.8 + - - -
499A GLU* 4.4 3.5 + - - +
501A VAL* 3.4 28.9 - - + +
512A LEU* 5.7 0.4 - - + -
1025A VAL* 4.0 22.4 - - + -
1026A ALA 3.5 1.3 - - - -
1027A TYR* 3.5 41.5 - + + -
1028A HIS* 6.2 0.2 - - - -
1033A VAL* 1.3 73.9 - - - +
1035A ALA* 1.3 59.4 + - - +
1036A VAL* 4.1 1.5 + - + -
1078A LEU* 3.3 9.7 - - - +
1079A ILE* 2.7 51.8 + - + +
1081A PRO* 3.6 29.6 - - + -
1084A TRP* 3.6 28.8 - + - -
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Residues in contact with ALA1035 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025A VAL* 3.4 4.2 - - - -
1026A ALA* 3.0 33.3 + - + +
1028A HIS* 6.3 0.7 - - + -
1034A TYR* 1.3 72.3 - - - +
1036A VAL* 1.3 59.8 + - - +
1076A ILE* 4.7 0.7 - - + -
1077A GLN 3.9 5.6 - - - +
1078A LEU* 4.6 2.0 - - + -
1103A MET* 3.6 26.7 - - + +
1121A VAL* 4.2 16.8 - - + -
1144A VAL* 6.3 0.9 - - + -
1160A PHE* 4.2 22.9 - - + -
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Residues in contact with VAL1036 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A LEU* 3.8 31.4 - - + -
1018A LEU* 4.4 12.8 - - + -
1022A ALA* 4.4 4.5 - - + -
1024A TYR 3.3 13.9 - - - +
1025A VAL* 3.8 17.3 - - + -
1034A TYR* 4.1 1.5 + - + -
1035A ALA* 1.3 77.5 - - - +
1037A ALA* 1.3 62.6 + - - +
1038A THR* 3.7 21.2 + - + -
1076A ILE* 3.3 4.4 - - - +
1077A GLN* 2.5 49.0 + - + +
1079A ILE* 3.8 13.0 - - + -
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Residues in contact with ALA1037 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023A HIS* 2.9 31.5 + - + +
1024A TYR* 3.4 18.9 + - + +
1036A VAL* 1.3 72.7 - - - +
1038A THR* 1.3 63.2 + - - +
1074A PHE* 5.7 0.4 - - + -
1075A SER 3.6 6.7 - - - +
1076A ILE* 4.3 3.8 - - + +
1100A VAL* 4.2 27.6 - - + -
1103A MET* 3.6 25.9 - - - -
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Residues in contact with THR1038 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018A LEU* 3.9 11.7 - - + -
1020A CYS* 3.7 26.9 - - - -
1021A THR 3.3 10.1 - - - +
1022A ALA* 4.5 0.4 - - - -
1023A HIS* 4.2 3.1 - - - -
1036A VAL* 3.7 19.1 - - + -
1037A ALA* 1.3 79.3 - - - +
1039A SER* 1.3 62.5 + - - +
1074A PHE* 3.3 12.6 - - - +
1075A SER* 2.8 47.3 + - - +
1077A GLN* 3.7 22.3 + - + -
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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