Contacts of the strand formed by residues 7002 - 7009 (chain A) in PDB entry 6W4H
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 ALA7002 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6968A LYS* 3.4 4.3 - - - +
6969A ILE* 2.8 39.9 + - + +
6990A ALA* 4.3 4.3 - - + -
6991A PHE 3.3 19.3 - - - +
6992A VAL* 4.1 5.6 - - + +
7000A SER 3.5 0.6 + - - -
7001A GLU* 1.3 73.3 - - - +
7003A PHE* 1.3 67.1 + - - +
7004A LEU 3.9 0.4 - - - -
7026A TYR* 3.1 36.8 - - + +
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Residues in contact with PHE7003 (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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6844A LYS* 4.1 26.5 - - + -
6845A TYR* 5.3 6.5 - + - -
6848A LEU* 3.9 46.7 - - + -
6926A ILE* 5.4 2.9 - - + -
6927A SER 4.1 7.9 - - - -
6928A ASP* 4.2 10.1 - - + -
6966A ALA* 4.4 8.3 - - + -
6967A ILE 3.6 2.5 - - - +
6968A LYS* 3.6 37.2 - - + -
6990A ALA* 3.5 1.5 - - - -
6991A PHE* 2.8 45.1 + + - +
6993A THR* 4.3 12.8 - - + -
7001A GLU* 4.1 19.5 - - + -
7002A ALA* 1.3 73.9 - - - +
7004A LEU* 1.3 63.0 - - - +
7005A ILE* 3.4 13.6 + - + +
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Residues in contact with LEU7004 (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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6965A VAL* 3.8 2.8 - - - +
6966A ALA* 3.3 2.1 + - - -
6967A ILE* 2.8 46.9 + - + +
6969A ILE* 3.5 46.0 - - + -
6975A ASN 6.3 0.2 - - - +
6978A LEU* 4.0 20.9 - - + -
6979A TYR* 3.7 37.9 - - + +
6982A MET* 4.3 13.7 - - + -
6988A TRP* 4.3 6.1 - - + -
6989A THR 3.5 3.1 - - - +
6990A ALA* 3.7 24.2 - - + -
7002A ALA 3.9 0.8 - - - -
7003A PHE* 1.3 69.2 - - - +
7005A ILE* 1.3 60.8 + - - +
7006A GLY 4.1 0.9 + - - -
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Residues in contact with ILE7005 (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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6848A LEU* 4.0 10.3 - - + -
6851A TYR* 3.7 22.2 - - + -
6852A LEU* 3.9 17.0 - - + -
6855A LEU* 3.8 23.1 - - + -
6857A LEU* 6.0 0.2 - - + -
6964A SER* 5.8 2.0 - - - -
6965A VAL 3.2 9.9 - - - +
6966A ALA* 4.0 13.9 - - + -
6982A MET* 3.7 3.3 - - - +
6987A TRP* 5.1 1.6 - - + -
6988A TRP* 3.0 9.7 - - - +
6989A THR* 2.8 42.1 + - + +
6991A PHE* 3.7 27.6 - - + -
7003A PHE* 3.7 7.9 - - + +
7004A LEU* 1.3 74.4 - - - +
7006A GLY* 1.3 67.0 + - - +
7007A CYS* 4.6 2.9 - - + +
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Residues in contact with GLY7006 (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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6964A SER* 3.1 8.3 - - - -
6965A VAL* 2.9 38.4 + - - +
6982A MET* 3.7 11.1 - - - -
6985A PHE* 3.2 30.8 - - - -
6987A TRP 3.8 2.7 - - - -
6988A TRP* 4.4 0.2 - - - -
7005A ILE* 1.3 72.0 - - - +
7007A CYS* 1.3 58.5 + - - -
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Residues in contact with CYS7007 (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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6855A LEU* 4.0 16.8 - - + -
6856A THR* 3.7 24.2 - - - -
6857A LEU* 4.2 3.1 - - - -
6964A SER* 3.4 9.4 - - - -
6985A PHE* 3.6 1.0 - - - -
6986A ALA* 3.2 14.4 + - - +
6987A TRP* 2.8 40.6 + - + +
7005A ILE* 4.0 1.7 - - + -
7006A GLY* 1.3 71.5 - - - -
7008A ASN* 1.3 92.5 + - - +
7105A BDF 3.8 11.7 - - - -
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Residues in contact with ASN7008 (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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6856A THR* 2.8 45.3 + - - +
6858A ALA 4.2 2.4 - - - +
6962A GLY 3.2 18.6 + - - -
6963A GLY 3.2 5.0 + - - -
6964A SER* 3.1 13.5 + - - -
6985A PHE* 3.8 1.1 - - - -
6986A ALA* 2.9 32.1 + - + +
7007A CYS* 1.3 76.6 - - - +
7009A TYR* 1.3 65.1 + - - +
7010A LEU* 3.6 4.8 + - - +
7073A LEU 3.1 23.1 + - - +
7074A SER 3.4 9.4 - - - +
7076A GLY* 3.6 10.9 + - - -
7105A BDF 4.3 1.4 + - - -
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Residues in contact with TYR7009 (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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6955A ILE* 3.8 22.7 - - + -
6956A GLN* 3.5 33.2 + - + +
6959A LEU* 3.6 42.0 - - + -
6960A ALA 3.8 7.4 - - - +
6961A LEU* 3.3 19.3 - - + +
6962A GLY 2.7 26.6 + - - +
6963A GLY 2.7 17.2 + - - +
6981A LEU* 5.7 1.1 - - + -
6984A HIS* 3.5 30.2 + - + -
6985A PHE* 3.5 22.2 - + + -
7008A ASN* 1.3 70.6 - - - +
7010A LEU* 1.3 61.1 + - - +
7011A GLY* 3.5 29.0 + - - -
7073A LEU* 4.5 1.0 - - - +
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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