Contacts of the strand formed by residues 627 - 634 (chain A) in PDB entry 4APT
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 VAL 627 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A ASP* 3.1 10.6 - - - +
622A SER* 3.1 29.9 + - - +
624A SER* 3.3 22.6 + - - +
625A PRO 3.1 16.2 - - - +
626A GLY* 1.3 81.9 - - - +
628A ALA* 1.3 62.9 + - - +
644A GLU* 3.7 21.1 - - + +
645A VAL 3.4 24.7 - - - +
646A LEU* 3.9 16.6 - - + -
647A VAL* 4.0 4.6 - - - +
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Residues in contact with ALA 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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619A ILE* 5.0 5.2 - - + -
620A GLU 3.4 15.3 - - - +
621A ASP* 4.5 2.9 - - - -
622A SER 3.9 1.6 - - - +
627A VAL* 1.3 75.7 - - - +
629A VAL* 1.3 62.7 + - - +
630A ILE* 3.9 2.2 + - + +
643A VAL 3.6 1.0 - - - +
645A VAL* 2.7 47.1 + - - +
647A VAL* 3.8 18.7 - - + +
661A CYS* 4.4 20.2 - - + -
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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
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618A ARG* 4.1 1.4 + - - +
619A ILE* 3.7 1.2 - - - -
620A GLU* 2.5 52.4 + - + +
621A ASP 4.4 2.0 - - - +
622A SER* 3.6 30.5 - - - +
623A HIS* 6.0 0.2 - - - +
628A ALA* 1.3 71.9 - - - +
630A ILE* 1.3 65.2 + - - +
631A GLN 4.3 0.3 + - - -
642A SER* 4.4 13.5 - - - -
643A VAL 3.4 20.0 - - - +
644A GLU* 3.7 18.8 - - + +
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Residues in contact with ILE 630 (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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616A VAL* 3.7 22.2 - - + -
618A ARG 3.3 14.8 - - - +
619A ILE* 4.1 8.1 - - + -
628A ALA 4.3 7.4 - - - +
629A VAL* 1.3 79.6 - - - +
631A GLN* 1.3 62.1 + - - +
632A PHE* 3.5 22.1 - - + -
641A VAL 3.7 0.5 - - - +
642A SER* 3.4 2.6 - - - -
643A VAL* 2.9 35.5 + - + +
645A VAL* 4.3 10.3 - - + -
651A PHE* 3.8 29.8 - - + -
661A CYS* 3.7 31.0 - - - -
677A LEU* 3.8 6.3 - - + -
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Residues in contact with GLN 631 (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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616A VAL* 3.8 3.8 - - - -
617A GLU* 2.9 49.4 + - + +
618A ARG* 2.9 40.2 + - + +
629A VAL 4.3 0.8 + - - -
630A ILE* 1.3 72.5 - - - +
632A PHE* 1.3 67.8 + - - +
640A GLN* 4.5 24.9 + - + +
641A VAL 3.5 10.5 - - - +
642A SER* 4.2 10.1 - - - +
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Residues in contact with PHE 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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614A SER* 3.7 23.6 - - - -
615A THR 3.6 2.5 - - - -
616A VAL* 3.6 23.8 - - + -
617A GLU* 4.6 1.6 - - - -
630A ILE* 3.5 36.8 - - + -
631A GLN* 1.3 79.9 + - - +
633A ALA* 1.3 59.1 + - - +
634A VAL* 3.8 17.3 - - + -
639A ALA 3.2 1.6 - - - +
640A GLN* 3.5 4.2 - - - -
641A VAL 2.7 36.9 + - - +
643A VAL* 3.8 20.9 - - + -
651A PHE* 3.6 30.7 - + - -
683A CYS* 4.0 9.4 - - - -
567B ALA* 3.9 6.7 - - + -
568B PRO* 3.8 19.5 - - + -
569B PRO* 4.5 0.2 - - + -
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Residues in contact with ALA 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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613A SER 4.1 0.5 - - - +
614A SER* 3.4 2.8 - - - -
615A THR* 2.9 34.1 + - - +
617A GLU* 4.1 8.5 - - + +
632A PHE* 1.3 71.0 - - - +
634A VAL* 1.3 61.7 + - - +
635A GLY 3.8 2.3 + - - +
638A ARG* 3.6 55.1 - - + +
639A ALA 3.3 5.2 - - - -
640A GLN* 4.9 1.8 - - + +
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Residues in contact with VAL 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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612A ASP* 4.0 13.0 - - - +
614A SER* 3.7 18.8 - - - +
632A PHE* 4.0 17.0 - - + -
633A ALA* 1.3 70.6 - - - +
635A GLY* 1.3 70.7 + - - +
636A GLU 3.6 3.6 - - - +
639A ALA* 2.7 43.1 + - - +
641A VAL* 4.0 15.7 - - + -
565B ALA* 3.7 23.3 - - + +
566B MET 3.7 24.5 - - - +
567B ALA* 4.3 1.8 - - - -
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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