Contacts of the strand formed by residues 628 - 636 (chain A) in PDB entry 1QWN
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 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A HIS* 3.2 8.3 - - - -
559A ASN 3.0 26.8 + - - -
624A VAL* 3.4 6.8 - - - +
625A PRO 3.1 10.4 + - - -
626A PRO 3.0 5.1 + - - -
627A MET* 1.3 80.7 - - - +
629A LEU* 1.3 64.1 + - - -
946A PHE* 3.2 19.1 - - - -
947A GLY* 4.5 0.4 - - - -
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Residues in contact with LEU 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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442A LEU* 4.1 4.5 - - + -
505A VAL* 4.1 18.4 - - + -
508A LEU* 3.8 40.8 - - + -
509A LEU* 3.9 26.0 - - + -
556A VAL* 3.9 11.9 - - + -
557A MET 3.2 10.5 - - - +
558A HIS* 3.5 34.8 - - + -
624A VAL* 4.0 0.6 - - - +
625A PRO* 3.6 4.2 - - - +
628A GLY* 1.3 74.7 - - - +
630A ALA* 1.3 61.6 + - - +
932A PHE* 4.9 0.2 - - + -
945A GLN* 3.3 12.2 - - - +
946A PHE* 2.9 39.0 + - + +
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Residues in contact with ALA 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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556A VAL* 3.4 3.3 - - - -
557A MET* 2.9 31.4 + - + +
623A ARG 3.5 24.9 - - - +
624A VAL* 4.2 13.2 - - + -
625A PRO* 4.4 2.0 - - + -
629A LEU* 1.3 76.8 - - - +
631A THR* 1.3 62.6 + - - +
632A TYR* 4.0 19.0 - - + +
944A GLY 3.7 6.1 - - - +
945A GLN* 5.2 3.6 - - + +
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Residues in contact with THR 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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509A LEU* 3.6 18.0 - - - +
554A HIS* 3.8 29.2 - - + -
555A VAL 3.4 12.1 - - - +
556A VAL* 3.8 2.4 - - - +
582A ASP* 4.0 2.3 - - - +
583A LEU* 3.6 28.0 + - + -
630A ALA* 1.3 69.9 - - - +
632A TYR* 1.3 72.6 + - - +
939A TRP* 4.2 10.3 - - + -
943A GLN 2.9 24.0 + - - +
944A GLY* 3.0 20.0 + - - +
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Residues in contact with TYR 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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554A HIS* 3.3 4.9 - - - -
555A VAL* 2.8 44.2 + - + -
557A MET* 3.5 27.4 - - + -
580A VAL* 4.1 4.0 - - + -
581A THR 3.3 17.0 - - - +
582A ASP* 3.9 16.3 - - + +
588A VAL* 3.8 24.2 - - + -
620A PHE* 3.7 22.0 - + + -
621A LYS 4.1 3.9 + - - -
622A ALA* 3.6 13.5 - - + -
623A ARG* 3.0 33.3 + - - +
630A ALA* 4.0 21.0 - - + +
631A THR* 1.3 76.6 - - - +
633A VAL* 1.3 67.4 + - - +
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Residues in contact with VAL 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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552A SER* 3.9 17.0 - - - +
553A LYS 3.4 7.6 - - - +
554A HIS* 3.7 22.2 - - + +
579A SER 3.6 1.0 - - - +
580A VAL* 3.3 7.3 - - - +
581A THR* 2.8 47.0 + - - +
582A ASP 4.9 1.8 - - - +
583A LEU* 3.6 27.4 - - + -
632A TYR* 1.3 81.0 - - - +
634A LEU* 1.3 65.8 + - - +
635A THR* 3.7 18.2 + - - +
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Residues in contact with LEU 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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543A ILE* 3.7 30.7 - - + -
545A LEU* 3.9 8.3 - - + +
552A SER* 3.0 6.3 - - - -
553A LYS* 2.9 40.3 + - + +
555A VAL* 4.5 11.9 - - + -
571A PHE* 4.4 6.5 - - + -
573A VAL* 4.0 17.9 - - + -
578A VAL* 3.9 12.1 - - + -
579A SER 3.4 2.7 - - - +
580A VAL* 3.5 31.0 - - + -
618A ILE* 4.2 12.1 - - + -
620A PHE* 4.2 15.0 - - + -
633A VAL* 1.3 74.5 - - - +
635A THR* 1.3 62.6 + - - +
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Residues in contact with THR 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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551A PRO* 3.5 14.8 - - + +
552A SER* 3.7 11.8 - - - -
577A PHE 3.9 0.2 - - - +
578A VAL* 3.3 7.4 - - - +
579A SER* 2.9 42.7 + - - +
581A THR* 4.9 5.1 + - - +
633A VAL* 3.7 11.4 + - - +
634A LEU* 1.3 75.9 + - - +
636A ILE* 1.3 74.6 + - - +
637A SER* 5.2 1.0 - - - -
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Residues in contact with ILE 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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545A LEU* 3.8 34.4 - - + +
546A GLY* 3.9 18.6 - - - +
547A GLU* 4.7 4.3 - - - +
551A PRO* 3.0 32.7 + - + +
575A SER* 3.6 29.4 - - - +
577A PHE 3.3 12.1 - - - +
578A VAL* 4.5 1.8 - - + +
635A THR* 1.3 88.1 - - - +
637A SER* 1.3 73.0 + - - +
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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