Contacts of the strand formed by residues 629 - 639 (chain A) in PDB entry 1QAS
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 GLU 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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627A ARG* 3.0 21.4 - - - +
628A PRO* 1.3 75.0 - - - +
630A ARG* 1.3 61.8 + - - +
631A LEU 4.0 0.7 - - - -
691A GLU* 2.7 19.0 - - - +
692A VAL* 2.9 18.2 + - - +
695A PRO* 3.4 25.4 - - + +
723A TRP* 3.6 27.8 - - + -
754A ILE* 3.4 14.4 - - + +
755A GLN 3.4 7.5 - - - +
756A ASP* 3.2 39.5 - - - +
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Residues in contact with ARG 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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629A GLU* 1.3 73.4 - - - +
631A LEU* 1.3 59.3 + - - +
632A ARG* 3.6 24.9 + - - +
689A GLU* 3.3 45.0 + - + +
690A PHE 3.5 4.9 - - - +
691A GLU* 3.1 35.2 + - - +
753A SER 3.3 3.8 - - - +
754A ILE* 4.5 0.7 - - - -
755A GLN* 2.8 41.5 + - + +
756A ASP* 5.1 6.7 + - - -
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Residues in contact with LEU 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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629A GLU 4.0 0.8 - - - -
630A ARG* 1.3 72.5 - - - +
632A ARG* 1.3 66.7 - - - +
633A VAL* 3.8 21.1 - - + -
660A ILE* 3.8 22.9 - - + -
688A PHE 3.9 0.2 - - - +
689A GLU* 3.3 4.0 - - - +
690A PHE* 2.9 46.0 + - + +
692A VAL* 4.9 0.2 - - + -
700A VAL* 3.9 11.7 - - + -
723A TRP* 3.5 32.3 - - + -
726A LEU* 3.7 22.4 - - + -
752A ILE* 3.7 15.0 - - + -
753A SER 3.2 9.0 - - - +
754A ILE* 3.9 8.5 - - + +
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Residues in contact with ARG 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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630A ARG* 3.6 23.0 + - + +
631A LEU* 1.3 77.5 - - - +
633A VAL* 1.3 62.8 + - - +
634A ARG* 4.2 0.4 - - - -
687A GLU* 3.3 32.0 + - - +
688A PHE 3.2 5.8 - - - +
689A GLU* 2.7 32.1 + - + +
751A LYS 3.7 0.9 - - - +
752A ILE* 3.5 3.8 - - - -
753A SER* 2.7 50.4 + - - +
755A GLN* 3.2 36.6 - - - +
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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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631A LEU* 3.8 29.6 - - + -
632A ARG* 1.3 79.2 - - - +
634A ARG* 1.3 62.9 + - - +
635A ILE* 3.8 16.2 - - + -
658A VAL* 4.7 17.0 - - + -
686A MET 3.7 2.3 - - - +
687A GLU* 3.2 3.2 - - - -
688A PHE* 2.7 43.8 + - + +
690A PHE* 4.7 3.8 - - + -
700A VAL* 5.0 1.3 - - + -
702A PHE* 3.7 31.9 - - + -
726A LEU* 5.6 0.7 - - + -
750A VAL* 4.5 2.0 - - + -
751A LYS 3.4 7.0 - - - +
752A ILE* 4.4 10.8 - - + -
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Residues in contact with ARG 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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632A ARG 6.0 0.2 - - - -
633A VAL* 1.3 71.6 - - - +
635A ILE* 1.3 62.1 + - - +
636A ILE* 3.2 14.4 + - + +
685A ASP* 2.9 56.9 + - - +
686A MET* 3.5 3.1 - - - +
687A GLU* 3.5 39.6 - - + +
750A VAL* 3.1 9.4 - - - +
751A LYS* 2.8 52.1 + - + +
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Residues in contact with ILE 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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633A VAL* 3.8 10.1 - - + -
634A ARG* 1.3 68.9 - - - +
636A ILE* 1.3 60.1 + - - +
637A SER 5.0 1.6 - - - +
656A VAL* 4.0 22.9 - - + -
658A VAL* 3.8 21.1 - - + -
672A THR* 4.3 9.4 - - + -
684A TRP* 3.6 28.6 - - + +
685A ASP 2.9 19.6 + - - -
686A MET 2.8 18.7 + - - +
688A PHE* 3.6 26.9 - - + -
702A PHE* 4.0 8.7 - - + -
748A LEU* 4.9 3.8 - - + -
749A PHE 4.9 1.3 - - - +
750A VAL* 3.5 25.1 - - + -
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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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213A GLU* 3.7 24.5 - - + -
634A ARG* 3.7 23.3 - - + +
635A ILE* 1.3 70.2 - - - +
637A SER* 1.3 55.1 + - - +
683A ARG* 3.4 6.4 - - - +
684A TRP* 2.8 31.5 + - - -
685A ASP* 3.0 28.4 + - - +
730A TYR* 4.0 15.0 - - + -
749A PHE* 3.0 48.3 + - + +
750A VAL 3.8 19.1 - - - -
751A LYS* 3.9 7.0 - - + +
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Residues in contact with SER 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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213A GLU* 3.6 28.0 + - - -
635A ILE* 5.0 0.9 - - - +
636A ILE* 1.3 79.9 - - - +
638A GLY* 1.3 57.2 + - - +
639A GLN* 2.7 26.8 + - - -
681A ASN 5.3 1.3 - - - -
682A PRO 3.2 13.7 - - - -
683A ARG* 4.1 6.1 - - - +
684A TRP* 3.7 8.6 - - - -
748A LEU* 3.3 4.9 - - - +
749A PHE* 2.6 41.1 + - - +
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Residues in contact with GLY 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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637A SER* 1.3 74.8 - - - +
639A GLN* 1.3 67.4 + - - +
641A LEU* 4.3 2.7 - - - -
681A ASN* 3.6 7.1 - - - -
682A PRO* 2.8 35.0 + - - +
684A TRP* 3.5 13.5 - - - -
747A THR 3.4 10.3 - - - -
748A LEU* 3.9 7.0 - - - -
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Residues in contact with GLN 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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211A ARG* 3.5 38.9 - - - +
280A LEU* 5.2 2.7 - - + -
637A SER* 2.7 30.3 + - - -
638A GLY* 1.3 81.4 + - - +
640A GLN* 1.3 73.5 + - + +
641A LEU* 3.3 4.3 + - - +
679A GLY 4.4 0.2 - - - -
680A PHE 3.4 7.6 - - - +
681A ASN* 5.5 0.2 - - - -
732A HIS* 3.5 3.5 - - + -
745A SER 3.3 6.6 - - - +
747A THR* 2.7 75.7 + - - +
748A LEU 3.3 0.5 + - - -
749A PHE* 3.2 12.2 + - - +
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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