Contacts of the strand formed by residues 636 - 643 (chain A) in PDB entry 4FOV
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 ILE 636 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU* 4.3 7.4 - - + -
553A ARG* 3.7 23.6 - - - +
555A PHE* 3.9 25.4 - - + -
608A VAL* 4.1 18.4 - - + -
627A GLY* 3.6 27.4 - - - -
628A LEU 3.4 2.5 - - - +
629A VAL* 4.4 11.9 - - + -
634A ASP 4.2 1.6 - - - +
635A SER* 1.3 79.3 - - - +
637A ASP* 1.3 61.7 + - - +
638A TRP* 3.5 43.4 + - + +
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Residues in contact with ASP 637 (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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628A LEU* 2.9 40.7 + - + +
630A ASN* 6.0 1.5 - - + +
635A SER 4.2 0.6 - - - -
636A ILE* 1.3 70.6 - - - +
638A TRP* 1.3 67.0 + - - +
639A LYS* 2.9 33.5 + - - +
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Residues in contact with TRP 638 (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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555A PHE* 3.8 22.2 - + - -
565A TYR* 5.9 1.9 - + - -
581A ILE* 3.7 48.8 - - + +
582A ASP 4.5 8.1 - - - +
584A ILE* 5.1 0.9 - - + -
608A VAL* 4.4 8.1 - - + -
610A LEU* 3.6 30.3 - - + -
625A VAL* 3.8 31.6 - - + -
626A VAL 3.7 2.0 - - - -
627A GLY* 3.5 31.0 - - - -
636A ILE* 3.5 35.4 + - + +
637A ASP* 1.3 72.2 + - - +
639A LYS* 1.3 60.1 + - - +
640A TYR 3.8 0.7 - - - -
641A HIS* 4.1 14.5 + - + +
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Residues in contact with LYS 639 (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 ASP* 2.4 36.2 + - - +
605A LYS* 4.9 5.3 - - - +
626A VAL 2.9 7.6 + - - +
628A LEU* 3.6 23.6 - - + +
637A ASP* 2.9 26.7 + - - +
638A TRP* 1.3 74.5 - - - +
640A TYR* 1.3 90.0 + - + +
641A HIS* 4.4 3.8 + - - -
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Residues in contact with TYR 640 (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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602A ILE* 4.4 7.2 - - + -
603A ASP* 2.6 34.3 + - - -
624A LEU 3.9 0.2 - - - +
625A VAL* 3.3 5.9 - - - +
626A VAL* 2.7 55.9 + - + +
628A LEU* 4.8 1.8 - - + -
639A LYS* 1.3 111.7 + - + +
641A HIS* 1.3 63.1 + - - +
642A TYR 4.1 0.4 - - - -
695A LEU 4.0 12.8 - - - +
696A THR* 3.7 49.4 - - + -
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Residues in contact with HIS 641 (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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583A GLY* 3.6 26.6 - - - -
584A ILE* 4.3 4.0 - - + -
614A ASN* 4.3 2.0 + - - -
623A GLN* 3.1 30.0 + - - +
624A LEU 3.6 4.5 - - - -
625A VAL* 3.7 25.2 - - + +
638A TRP* 4.1 19.2 + - + +
639A LYS 4.8 2.7 - - - -
640A TYR* 1.3 80.8 - - - +
642A TYR* 1.3 60.7 + - - +
643A ASP* 3.9 6.6 + - - +
695A LEU 4.6 4.8 - - - +
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Residues in contact with TYR 642 (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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137A HIS* 4.2 5.0 + - - -
138A LYS* 2.8 41.4 + - - -
139A GLY 4.7 4.0 - - - -
623A GLN* 3.1 7.9 - - - +
624A LEU* 2.7 41.9 + - + +
626A VAL* 6.1 0.2 - - - +
640A TYR 4.1 0.6 - - - -
641A HIS* 1.3 71.1 - - - +
643A ASP* 1.3 81.6 + - - +
644A ILE* 3.8 21.6 + - + -
688A ILE* 5.4 0.8 - - + +
690A LEU* 3.6 32.4 - - + +
694A ASP* 3.4 27.6 - - + -
695A LEU* 3.7 36.1 - - + +
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Residues in contact with ASP 643 (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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136A LYS* 6.0 2.1 - - - +
137A HIS* 6.0 0.2 - - - -
138A LYS 5.5 0.3 + - - -
622A GLY 3.6 5.6 - - - +
623A GLN* 3.3 25.6 + - - +
641A HIS* 3.9 7.6 + - - +
642A TYR* 1.3 92.6 + - - +
644A ILE* 1.3 64.2 + - - +
645A ASP* 3.4 14.2 + - - +
647A PRO* 5.8 9.6 - - + -
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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