Contacts of the strand formed by residues 631 - 636 (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 MET 631 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASP* 3.7 37.7 - - + +
170A ILE* 4.4 4.0 - - - -
173A SER* 3.2 30.3 - - - +
601A GLN 3.1 4.3 + - - +
602A VAL* 3.4 7.3 - - + -
603A TYR* 2.9 26.7 + - - +
629A LEU* 3.4 0.9 - - - +
630A LYS* 1.3 82.2 - - - +
632A ILE* 1.3 84.3 + - - +
633A PHE* 3.9 22.2 - - + -
647A ASP* 3.2 16.2 - - + -
648A ILE* 3.9 17.3 - - + -
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Residues in contact with ILE 632 (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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153A ARG* 3.7 28.3 - - - +
603A TYR* 3.4 15.9 - - + -
605A LEU* 3.9 22.0 - - + -
626A PHE* 3.6 38.6 - - + -
629A LEU* 3.7 17.5 - - + -
631A MET* 1.3 78.8 - - - +
633A PHE* 1.3 63.7 + - - +
642A SER 5.4 0.2 - - - +
645A TYR 3.8 9.6 - - - +
646A ALA* 3.6 18.5 - - - +
647A ASP* 2.7 41.5 + - - +
648A ILE 3.2 4.9 + - - -
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Residues in contact with PHE 633 (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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170A ILE* 3.6 46.4 - - + -
174A ILE* 5.0 1.3 - - + -
186A PHE* 4.1 8.7 - + - -
206A MET* 5.4 1.3 - - - -
602A VAL* 3.7 22.0 - - + -
603A TYR 3.1 13.3 + - - +
604A MET* 3.5 46.1 - - + -
605A LEU* 2.8 34.9 + - - +
631A MET* 3.9 16.2 - - + -
632A ILE* 1.3 75.6 - - - +
634A ALA* 1.3 53.1 + - - +
635A LEU* 3.8 18.8 - - + -
646A ALA* 4.7 0.2 - - - -
648A ILE* 3.2 14.8 - - + +
650A LEU* 4.5 1.1 - - + -
694A ILE* 3.9 15.5 - - + -
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Residues in contact with ALA 634 (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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605A LEU* 3.3 27.6 - - + -
633A PHE* 1.3 75.1 - - - +
635A LEU* 1.3 60.3 + - - +
636A GLU* 4.3 10.1 - - + -
643A ALA* 4.3 20.2 - - + -
646A ALA* 4.5 2.0 - - + +
648A ILE 2.9 10.3 + - - +
649A VAL* 3.5 7.1 - - + -
650A LEU* 2.7 36.4 + - - +
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Residues in contact with LEU 635 (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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604A MET* 4.0 12.3 - - + -
605A LEU 2.8 18.4 + - - +
606A LEU* 4.0 18.0 - - + +
607A SER 4.6 0.7 + - - -
633A PHE* 3.8 29.8 - - + -
634A ALA* 1.3 73.9 - - - +
636A GLU* 1.3 62.2 + - - +
650A LEU* 3.7 21.5 - - + -
652A CYS* 3.8 9.9 - - - -
687A GLU* 4.2 12.8 - - + +
690A ALA* 4.0 18.6 - - + -
691A ILE* 3.8 33.7 - - + -
694A ILE* 4.7 1.6 - - + -
1987A MD1 2.8 18.2 + - - -
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Residues in contact with GLU 636 (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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143A VAL* 3.3 14.6 - - + +
605A LEU* 5.6 2.5 - - + +
607A SER 5.6 1.6 + - - -
608A GLN 4.7 4.9 + - - +
634A ALA* 3.7 7.6 - - + -
635A LEU* 1.3 78.5 - - - +
637A THR* 1.3 71.1 + - - +
638A ARG 3.1 26.1 + - - +
640A SER* 3.6 8.6 + - - +
643A ALA* 4.3 14.8 - - + -
649A VAL* 4.3 11.2 - - + -
650A LEU 3.1 11.1 + - - +
652A CYS* 2.9 22.0 + - - -
1987A MD1 2.6 64.3 + - - +
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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