Contacts of the helix formed by residues 628 - 638 (chain A) in PDB entry 2R92
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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588A LEU* 4.8 2.2 - - - -
590A ARG* 6.3 0.4 - - - -
620A LYS 4.3 6.3 - - - -
621A THR* 4.8 1.8 - - - -
623A GLY 5.0 2.9 - - - -
625A SER* 3.3 24.1 + - - -
626A ASN 2.6 16.1 + - - -
627A GLY* 1.3 72.1 - - - +
629A LEU* 1.3 63.5 + - - -
630A ILE 3.3 2.5 - - - -
631A HIS* 3.9 2.7 - - - -
632A VAL* 2.9 30.6 + - - +
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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
----------------------------------------------------------
582A ILE* 4.4 24.7 - - + -
586A ILE* 4.2 21.8 - - + -
588A LEU* 4.6 11.4 - - + +
607A ILE* 4.5 16.6 - - + -
617A VAL* 6.0 1.8 - - + -
621A THR* 3.0 25.4 + - + +
622A VAL* 3.9 22.6 - - + +
628A GLY* 1.3 71.0 - - - -
630A ILE* 1.3 60.3 + - - +
632A VAL* 3.1 6.7 + - + +
633A VAL* 2.8 49.4 + - + +
645A LEU* 4.2 17.0 - - + -
649A ILE* 4.4 6.3 - - + -
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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
----------------------------------------------------------
511A ILE* 4.1 10.8 - - + -
519A PRO* 4.4 6.3 - - + -
521A MET 3.5 15.7 - - - +
522A GLY* 3.6 6.7 - - - -
523A ILE* 4.6 3.4 - - + -
622A VAL* 3.5 31.0 - - + +
623A GLY 4.2 9.8 + - - +
624A SER* 5.2 0.2 - - - -
628A GLY 3.3 0.2 - - - -
629A LEU* 1.3 79.1 - - + +
631A HIS* 1.3 64.3 + - - +
632A VAL 3.1 0.5 + - - -
633A VAL* 3.2 8.1 + - - +
634A THR* 3.0 30.0 + - - +
642A CYS* 3.6 21.5 - - - -
645A LEU* 5.0 8.3 - - + -
646A PHE* 3.2 36.3 - - + -
649A ILE* 6.1 1.3 - - + -
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Residues in contact with HIS 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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512A VAL* 3.7 20.3 - - + +
517A ASN 4.1 17.4 + - - -
519A PRO* 3.5 30.2 - - + +
626A ASN* 2.6 41.0 + - - +
627A GLY* 4.0 7.2 - - - -
628A GLY 3.7 7.7 - - - +
629A LEU 3.3 0.4 - - - -
630A ILE* 1.3 78.9 - - - +
632A VAL* 1.3 63.7 + - + +
634A THR* 3.8 4.7 + - - -
635A ARG* 3.6 24.8 + - + +
876A ALA 5.3 2.5 - - - -
878A ILE 4.6 1.6 - - - -
879A GLU* 3.7 38.9 - - + +
962A ARG* 5.5 0.2 + - - -
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Residues in contact with VAL 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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586A ILE* 4.2 17.3 - - + -
587A HIS 4.4 10.8 - - - +
588A LEU* 4.0 21.3 - - + -
627A GLY* 4.1 7.4 - - - +
628A GLY 2.9 17.0 - - - +
629A LEU* 3.1 8.6 + - + +
631A HIS* 1.3 75.0 - - + +
633A VAL* 1.3 67.4 + - - +
634A THR 3.0 0.7 + - - -
635A ARG* 3.2 3.3 + - - +
636A GLU* 2.8 33.6 + - + +
962A ARG* 3.9 37.7 - - - +
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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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583A PRO* 4.2 17.0 - - + -
586A ILE* 3.5 22.9 - - + -
629A LEU* 2.8 42.2 - - + +
630A ILE* 3.7 3.8 - - - +
632A VAL* 1.3 74.2 - - - +
634A THR* 1.3 58.6 + - - +
637A LYS* 2.5 43.7 + - + +
638A GLY 3.5 0.9 + - - +
641A VAL* 4.4 2.9 - - + -
642A CYS* 4.2 18.4 - - - -
645A LEU* 3.7 23.6 - - + -
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Residues in contact with THR 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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508A PRO 5.4 0.9 - - - +
511A ILE* 3.5 25.3 - - + +
512A VAL* 4.5 16.6 - - + +
630A ILE 3.0 12.3 + - - -
631A HIS* 3.8 6.0 - - - -
632A VAL 3.0 0.2 + - - -
633A VAL* 1.3 75.4 - - - +
635A ARG* 1.3 72.9 + - - +
638A GLY* 2.9 42.9 + - - +
639A PRO* 4.7 9.6 - - + -
642A CYS* 2.8 24.7 - - + +
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Residues in contact with ARG 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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512A VAL* 4.3 10.9 - - + +
631A HIS* 3.6 20.3 + - + +
632A VAL 3.2 5.6 + - - +
634A THR* 1.3 92.0 + - - +
636A GLU* 1.3 64.1 + - - +
637A LYS 4.9 0.3 - - - -
638A GLY* 4.5 1.6 + - - -
876A ALA* 3.2 36.5 + - - +
877A HIS* 3.5 40.0 + - - +
878A ILE 5.7 0.2 - - - +
879A GLU* 4.1 16.8 - - - +
962A ARG* 4.3 13.5 - - - +
1052A GLN* 5.6 3.6 + - - -
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Residues in contact with GLU 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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585A GLY 5.3 6.5 - - - +
586A ILE* 4.3 13.7 - - + -
587A HIS 6.0 0.2 - - - +
632A VAL* 2.8 30.8 + - + +
633A VAL* 3.7 3.6 - - - +
635A ARG* 1.3 77.2 - - - +
637A LYS* 1.3 70.6 + - + +
962A ARG* 2.7 32.1 + - - -
966A ASN* 3.3 28.0 + - - +
1052A GLN* 5.9 2.6 + - - -
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Residues in contact with LYS 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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583A PRO* 4.7 7.2 - - + -
584A ASN* 3.0 32.3 + - - +
585A GLY* 4.9 4.3 - - - -
586A ILE* 4.6 10.5 - - + +
633A VAL* 2.5 27.3 + - + +
635A ARG 4.9 0.4 - - - -
636A GLU* 1.3 85.0 - - + +
638A GLY* 1.3 57.2 + - - +
641A VAL* 3.6 41.2 - - + +
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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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633A VAL 3.5 0.4 + - - +
634A THR* 2.9 22.0 + - - +
635A ARG 4.5 0.8 + - - -
636A GLU 3.8 0.2 - - - -
637A LYS* 1.3 80.2 - - - +
639A PRO* 1.3 75.5 - - - +
640A GLN 3.2 2.2 - - - -
641A VAL* 4.1 3.8 - - - -
642A CYS* 3.4 21.1 + - - +
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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