Contacts of the strand formed by residues 657 - 661 (chain A) in PDB entry 2IVF
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 GLU 657 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.7 16.8 - - + +
138A TYR* 5.3 3.3 + - - -
142A ARG* 2.8 46.0 + - - -
653A ALA* 3.7 3.2 - - + +
654A TRP 2.8 21.6 + - - +
655A TYR 3.9 7.0 - - - +
656A TYR* 1.3 81.4 - - - +
658A LYS* 1.3 61.3 + - - +
676A ARG* 3.6 12.1 + - - +
678A VAL* 3.4 28.3 - - + +
679A ALA 4.4 1.7 - - - +
680A PRO* 3.5 29.2 - - + +
681A PRO* 3.4 17.3 - - - +
686A GLU* 4.6 1.0 - - - +
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Residues in contact with LYS 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 5.1 1.8 - - + -
195A ALA 2.9 28.6 + - - -
653A ALA* 2.7 36.9 + - + +
654A TRP 3.8 12.8 - - - +
655A TYR* 4.8 5.8 - - - +
656A TYR 3.5 1.2 + - - -
657A GLU* 1.3 81.3 - - - +
659A HIS* 1.3 64.2 + - - +
660A GLU* 3.4 10.5 + - + +
674A VAL* 3.6 13.2 - - - +
675A ASP 3.7 5.4 - - - +
676A ARG* 4.0 9.3 - - - +
686A GLU* 3.6 24.9 - - + +
687A GLU* 2.9 19.7 + - - +
736A ASN* 3.7 22.0 - - - +
1987A MD1 2.9 15.0 + - - -
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Residues in contact with HIS 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.5 2.9 - - - +
658A LYS* 1.3 72.4 - - - +
660A GLU* 1.3 60.0 + - - +
673A PHE* 4.3 3.6 - + - -
674A VAL 3.2 7.6 - - - +
675A ASP* 3.6 25.4 + - - -
676A ARG* 3.5 30.4 - - + +
686A GLU* 4.2 4.0 + - - -
736A ASN* 2.9 30.6 + - - +
737A GLU* 3.5 49.9 + - + +
740A LEU* 3.9 14.8 - - + -
759A TYR* 3.6 19.5 - - - -
763A LYS* 6.1 0.4 - - + -
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.9 30.1 - - + -
195A ALA 4.2 0.9 - - - +
196A GLY* 3.1 20.8 - - - -
197A SER* 2.9 17.0 + - - -
198A ILE* 2.8 43.6 + - - +
199A ALA 3.8 1.2 + - - -
658A LYS* 4.2 10.1 - - + +
659A HIS* 1.3 80.2 - - - +
661A MET* 1.3 77.6 + - - +
673A PHE* 3.8 1.6 - - - -
674A VAL* 2.9 34.2 + - + +
736A ASN* 3.9 8.1 + - - +
740A LEU* 3.6 14.5 - - - +
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Residues in contact with MET 661 (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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83A LEU* 3.7 9.0 - - - +
197A SER* 3.7 9.3 + - - +
487A ASN* 3.4 29.6 - - - +
660A GLU* 1.3 92.0 + - - +
662A THR* 1.3 67.7 + - - +
663A THR* 4.3 2.1 - - - +
671A PHE* 3.6 29.6 - - + -
672A THR 3.2 5.2 - - - +
674A VAL 4.7 0.2 - - - +
740A LEU* 3.6 13.2 - - + +
743A MET* 4.1 19.1 - - + +
744A VAL* 4.8 2.7 - - - -
747A ASN* 3.8 11.0 - - - +
753A PHE* 4.0 13.0 - - - -
762A PHE* 3.6 34.5 - - + -
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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