Contacts of the strand formed by residues 622 - 629 (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 GLY 622 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A THR 3.8 1.3 - - - -
613A PRO* 4.2 0.2 - - - -
620A LYS 3.5 1.4 - - - -
621A GLY* 1.3 76.2 - - - +
623A GLN* 1.3 64.2 + - - +
643A ASP* 3.6 2.4 - - - +
644A ILE* 2.8 30.9 + - - +
645A ASP 4.3 3.9 + - - +
646A LEU 4.8 2.0 + - - -
649A TYR 4.6 1.2 + - - -
651A TYR* 3.2 40.9 - - - +
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Residues in contact with GLN 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LEU 3.6 0.5 - - - +
611A SER* 3.4 5.0 + - - -
612A THR* 2.9 38.2 + - + +
614A ASN* 3.1 33.3 + - + +
621A GLY* 3.7 6.3 + - - +
622A GLY* 1.3 80.4 - - - +
624A LEU* 1.3 66.2 + - - +
625A VAL* 3.8 12.4 - - + +
641A HIS* 3.1 34.5 + - - +
642A TYR 3.1 12.3 - - - +
643A ASP* 3.3 21.7 + - - +
644A ILE* 3.9 2.9 - - - +
651A TYR* 4.5 0.9 + - - -
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A ILE* 4.2 12.1 - - + -
610A LEU 3.2 4.9 - - - +
611A SER* 3.6 31.4 - - - +
623A GLN* 1.3 77.0 - - - +
625A VAL* 1.3 59.9 + - - +
626A VAL* 4.1 2.5 + - - +
640A TYR 3.9 0.5 - - - +
641A HIS* 3.6 1.0 - - - -
642A TYR* 2.7 42.2 + - + +
644A ILE* 3.9 19.9 - - + +
651A TYR* 4.2 1.6 - - - +
656A ILE* 4.2 8.3 - - + -
664A ILE* 4.2 11.7 - - + -
666A VAL* 4.0 10.5 - - + -
690A LEU* 3.7 26.5 - - + -
695A LEU* 3.7 27.8 - - + -
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Residues in contact with VAL 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ILE* 3.9 25.1 - - + -
608A VAL 3.8 0.2 - - - +
609A ILE* 3.4 3.4 - - - -
610A LEU* 2.8 42.1 + - + +
612A THR* 4.8 6.5 - - + -
623A GLN* 3.8 27.6 - - + +
624A LEU* 1.3 77.0 - - - +
626A VAL* 1.3 63.2 + - - +
627A GLY 3.8 1.0 + - - -
638A TRP* 3.8 30.6 - - + -
640A TYR 3.3 9.4 - - - +
641A HIS* 3.7 23.3 - - + +
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Residues in contact with VAL 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A ILE* 4.0 27.1 - - + -
607A ALA* 4.4 3.4 - - + -
608A VAL 3.6 8.5 - - - +
609A ILE* 4.4 9.4 - - + +
624A LEU 5.0 1.8 - - - +
625A VAL* 1.3 74.3 - - - +
627A GLY* 1.3 66.5 + - - +
628A LEU* 4.6 4.5 - - + -
638A TRP* 3.7 3.1 - - - -
639A LYS* 2.9 26.3 + - - +
640A TYR* 2.7 41.8 + - + +
642A TYR 6.1 0.2 - - - +
692A ILE* 5.5 0.4 - - + -
695A LEU* 3.8 38.8 - - + -
696A THR* 5.1 2.9 - - + -
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Residues in contact with GLY 627 (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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607A ALA* 3.2 6.6 - - - +
608A VAL* 2.8 38.6 + - - +
626A VAL* 1.3 73.7 - - - +
628A LEU* 1.3 63.5 + - - -
629A VAL 4.1 0.3 + - - -
636A ILE* 3.6 9.4 - - - -
637A ASP 3.3 8.7 - - - -
638A TRP* 3.5 22.4 - - - -
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Residues in contact with LEU 628 (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* 3.5 45.3 - - + +
603A ASP* 3.8 11.7 - - + +
605A LYS* 3.7 28.7 - - + +
606A GLU 3.4 3.4 - - - +
607A ALA* 3.9 10.3 - - + -
626A VAL* 4.6 5.2 - - + +
627A GLY* 1.3 79.3 - - - +
629A VAL* 1.3 64.0 + - - +
630A ASN* 3.7 0.7 + - - +
636A ILE* 3.4 2.3 - - - -
637A ASP* 2.9 42.7 + - + +
639A LYS* 3.6 33.9 - - + +
640A TYR* 4.8 1.3 - - + -
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Residues in contact with VAL 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A LEU* 4.1 31.2 - - + +
597A LYS* 5.3 1.3 - - - -
605A LYS* 4.1 18.7 - - - +
606A GLU* 2.8 40.8 + - + +
608A VAL* 4.3 11.7 - - + -
627A GLY 5.0 0.4 - - - +
628A LEU* 1.3 73.0 - - - +
630A ASN* 1.3 66.5 + - - +
631A LYS* 3.7 15.9 + - - +
634A ASP* 3.9 29.4 - - - +
635A SER 3.5 9.6 - - - +
636A ILE* 4.4 6.3 - - + +
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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