Contacts of the strand formed by residues 1004 - 1009 (chain A) in PDB entry 6PAI
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 VAL1004 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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955A SER* 2.8 35.4 + - - -
956A ALA* 4.0 2.9 - - + -
968A ALA* 3.7 22.1 - - + +
969A GLU 5.3 0.4 + - - -
974A LEU* 4.3 4.0 - - + -
1000A LEU* 3.8 20.4 - - + -
1002A GLU 4.1 1.3 + - - +
1003A PHE* 1.3 74.2 - - - +
1005A ASN* 1.3 60.9 + - - +
1006A VAL 3.4 26.2 - - - +
1007A PHE* 3.8 19.1 - - + -
1030A PHE* 3.5 35.2 - - + -
1031A GLY 3.6 4.0 - - - +
1032A THR* 4.3 2.0 - - + -
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Residues in contact with ASN1005 (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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358A PRO* 4.7 0.6 - - - +
359A ILE 2.9 29.9 + - - +
360A VAL* 3.7 22.7 - - - +
913A TYR* 5.9 0.3 - - - -
955A SER* 4.2 7.0 - - - +
956A ALA* 4.1 10.4 - - - +
1003A PHE* 3.5 24.4 + - - -
1004A VAL* 1.3 74.1 - - - +
1006A VAL* 1.3 61.9 + - + +
1031A GLY 2.8 7.5 + - - +
1033A VAL* 4.0 11.0 - - - +
44C LYS* 2.8 45.4 + - + +
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Residues in contact with VAL1006 (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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359A ILE* 4.1 10.1 - - + -
361A ASP* 3.6 31.0 - - - +
362A MET* 3.6 39.9 - - + +
956A ALA* 4.6 1.1 - - - -
1004A VAL* 3.4 4.0 - - - +
1005A ASN* 1.3 82.6 - - + +
1007A PHE* 1.3 75.1 + - - +
1008A CYS* 4.9 1.1 - - + -
1030A PHE* 3.2 10.8 - - - +
1031A GLY* 3.1 40.1 + - - +
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Residues in contact with PHE1007 (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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915A LYS* 3.2 23.6 + - - +
956A ALA* 3.6 28.8 - - + +
957A VAL 3.8 14.8 - - - +
958A GLU* 3.5 21.7 - - + +
966A LEU* 3.6 29.2 - - + -
967A GLY 4.5 0.4 - - - -
968A ALA* 3.8 29.4 - - + -
974A LEU* 3.9 12.1 - - + -
1004A VAL* 3.8 9.4 - - + -
1006A VAL* 1.3 78.1 - - - +
1008A CYS* 1.3 63.6 + - - +
1028A VAL* 3.7 15.5 - - + -
1029A LEU 3.5 1.3 - - - -
1030A PHE* 3.5 35.0 - + + -
1040A VAL* 4.9 2.0 - - + -
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Residues in contact with CYS1008 (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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362A MET* 3.8 24.9 - - + -
363A CYS* 4.1 12.1 - - - -
364A VAL* 3.6 37.5 - - + -
958A GLU* 3.9 2.0 + - - -
1006A VAL* 4.9 0.2 - - + -
1007A PHE* 1.3 78.2 - - - +
1009A HIS* 1.3 66.0 + - - +
1010A GLY 3.5 0.3 + - - -
1028A VAL* 3.2 7.9 - - - +
1029A LEU* 2.7 43.8 + - + +
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Residues in contact with HIS1009 (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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364A VAL* 3.9 12.9 - - - +
958A GLU* 3.2 33.2 + - + -
959A ILE 2.9 29.6 + - - -
960A LEU* 4.5 9.6 - - - -
1008A CYS* 1.3 75.5 - - - +
1010A GLY* 1.3 58.7 + - - +
1026A GLY* 6.1 0.4 - - - -
1027A SER 3.4 9.3 + - - +
1028A VAL* 3.7 21.3 - - + +
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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