Contacts of the strand formed by residues 631 - 635 (chain A) in PDB entry 1FO4
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 PHE 631 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A VAL* 5.3 2.5 - - + -
625A ALA* 3.5 33.9 - - + +
626A GLN* 3.6 38.4 - - + +
628A VAL* 3.1 21.1 + - + +
629A PRO 3.2 2.0 + - - -
630A GLY* 1.3 79.4 - - - +
632A VAL* 1.3 65.4 + - - +
633A CYS* 3.4 41.3 - - - -
634A PHE* 3.5 10.8 - - + -
670A VAL* 4.0 15.9 - - + -
671A VAL 4.3 2.0 - - - -
672A ALA* 4.4 4.0 - - - -
681A ALA* 4.0 11.9 - - + -
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Residues in contact with VAL 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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603A LEU* 4.3 23.1 - - + -
630A GLY 3.5 13.9 - - - +
631A PHE* 1.3 83.0 - - - +
633A CYS* 1.3 72.8 + - + +
671A VAL* 2.9 29.1 + - + +
672A ALA* 4.0 11.9 - - - -
673A ASP* 4.3 2.9 - - + +
819A THR* 4.3 7.6 - - + -
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Residues in contact with CYS 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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631A PHE* 3.4 19.2 - - - -
632A VAL* 1.3 90.4 - - + +
634A PHE* 1.3 61.5 + - - +
635A LEU* 4.1 20.2 - - - -
669A ALA 3.8 0.2 - - - +
670A VAL* 3.3 3.5 - - - -
671A VAL* 2.8 56.1 + - - +
818A LYS* 5.6 2.2 - - - -
819A THR* 4.5 10.3 - - - -
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Residues in contact with PHE 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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608A VAL* 3.9 26.2 - - + -
620A ILE* 4.0 32.3 - - + -
622A VAL* 3.8 28.0 - - + -
631A PHE* 3.5 13.4 - - + -
633A CYS* 1.3 77.1 - - - +
635A LEU* 1.3 70.3 + - - +
636A SER* 3.8 23.3 - - - -
639A ASP* 3.8 7.6 - - - +
667A ILE* 5.0 1.3 - - + -
668A GLY* 4.2 8.3 - - - -
669A ALA 3.2 21.3 - - - -
670A VAL* 4.1 10.3 - - + +
685A VAL* 4.2 9.9 - - + -
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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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605A LEU* 4.7 7.6 - - + -
633A CYS* 4.1 14.8 - - - -
634A PHE* 1.3 79.7 - - - +
636A SER* 1.3 62.4 + - - +
639A ASP* 3.4 16.8 - - + -
655A PHE* 4.2 15.9 - - + -
668A GLY* 3.0 6.1 - - - -
669A ALA* 2.6 39.1 + - + +
671A VAL* 3.8 13.7 - - + -
811A ALA 4.7 1.3 - - - +
814A LEU* 4.3 7.6 - - + -
815A ALA* 3.6 39.7 - - + +
818A LYS* 3.9 30.7 - - + -
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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