Contacts of the strand formed by residues 954 - 959 (chain A) in PDB entry 3I7K
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 MET 954 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912A LEU* 5.2 0.9 - - - +
913A TYR* 3.1 25.1 + - + -
925A ASP* 3.2 29.9 + - + +
928A ARG* 4.4 4.0 + - - +
929A SER 4.2 4.5 - - - +
930A VAL* 3.6 25.6 - - + -
952A ASN* 3.0 21.9 + - - +
953A TRP* 1.3 71.4 - - - +
955A SER* 1.3 55.6 + - - +
956A ALA 3.2 28.3 - - - +
957A VAL* 3.6 4.9 - - + -
967A GLY* 3.4 21.1 - - - -
968A ALA 3.4 11.2 - - - +
969A GLU* 4.2 0.7 - - - +
975A PHE* 3.5 26.7 - - + -
94B ARG* 2.7 22.5 + - - -
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Residues in contact with SER 955 (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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913A TYR* 3.4 28.4 + - - -
954A MET* 1.3 72.7 - - - +
956A ALA* 1.3 65.5 + - - +
968A ALA* 2.8 23.7 + - - +
969A GLU* 3.6 5.7 + - - -
1003A PHE* 3.4 32.0 - - - -
1004A VAL 2.8 26.6 + - - +
1005A ASN* 4.4 7.3 - - - +
94B ARG* 4.1 1.6 - - - +
95B GLN* 4.8 4.2 + - - -
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Residues in contact with ALA 956 (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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913A TYR* 4.1 11.4 - - - -
954A MET* 3.2 24.7 - - - +
955A SER* 1.3 80.5 + - - +
957A VAL* 1.3 62.5 + - - +
968A ALA* 3.2 8.6 + - + -
1004A VAL* 3.7 15.5 - - + +
1005A ASN 4.0 17.3 - - - +
1006A VAL* 4.3 1.6 - - - +
1007A PHE* 3.6 24.5 - - + +
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Residues in contact with VAL 957 (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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913A TYR* 4.3 20.9 - - + +
914A LEU 4.7 0.4 - - - -
915A LYS* 3.2 35.6 + - + +
923A VAL* 3.9 32.5 - - + +
924A GLY 4.3 10.1 - - - +
925A ASP* 5.5 0.4 - - + -
930A VAL* 4.2 16.8 - - + -
954A MET* 3.6 22.2 - - + -
956A ALA* 1.3 83.0 - - - +
958A GLU* 1.3 64.7 + - - +
966A LEU 3.4 9.4 - - - +
1007A PHE* 3.4 5.8 - - - -
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Residues in contact with GLU 958 (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* 3.1 33.8 + - - +
923A VAL* 4.8 4.4 - - - +
957A VAL* 1.3 77.7 - - - +
959A ILE* 1.3 84.8 + - - +
960A LEU* 3.6 1.5 + - + -
965A PHE* 3.4 5.2 - - - +
966A LEU* 2.6 48.4 + - + +
1007A PHE* 3.7 23.0 - - + +
1008A CYS* 3.6 17.8 - - - -
1009A HIS* 3.4 31.9 + - + +
1028A VAL* 4.4 13.2 - - + -
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Residues in contact with ILE 959 (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* 3.6 6.7 - - + -
916A THR* 3.2 47.8 - - - +
917A LYS* 3.4 34.5 - - + +
923A VAL* 3.1 29.2 - - + -
958A GLU* 1.3 80.5 + - - +
960A LEU* 1.3 59.8 + - - +
961A ASP* 3.1 29.4 - - - +
964A ASN 4.0 3.6 - - - -
965A PHE* 4.6 2.2 - - + -
1009A HIS* 2.9 32.9 + - - +
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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