Contacts of the strand formed by residues 630 - 639 (chain A) in PDB entry 1DQ8
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 ARG 630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A LYS* 3.9 5.2 - - - +
623A ASP* 3.4 9.2 - - - +
627A ARG* 3.3 24.8 + - - +
628A PHE* 3.2 24.1 + - - +
629A ALA* 1.3 78.3 - - - +
631A LEU* 1.3 66.6 + - - +
632A GLN* 3.0 9.9 + - - +
649A SER* 3.3 19.0 + - - -
650A ARG* 3.8 19.5 + - + +
831A PRO* 6.2 2.4 - - - +
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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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615A PHE* 3.8 22.1 - - + -
618A ILE* 3.9 20.6 - - + -
619A LYS* 3.0 53.6 + - + +
622A PHE* 4.0 19.7 - - + -
623A ASP* 2.8 17.8 + - - +
629A ALA 4.0 0.2 - - - -
630A ARG* 1.3 66.9 - - - +
632A GLN* 1.3 61.3 + - - +
633A LYS 3.8 12.8 - - - +
634A LEU* 4.1 4.9 - - + -
647A PHE* 3.9 19.3 - - + -
648A GLN 3.6 25.6 - - - +
649A SER* 3.8 3.9 - - - -
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Residues in contact with GLN 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 ASP 2.8 30.3 + - - +
587A GLY* 3.6 1.4 - - - -
615A PHE* 3.9 5.6 - - - -
630A ARG 3.0 10.4 + - - +
631A LEU* 1.3 74.1 - - - +
633A LYS* 1.3 78.1 + - + +
648A GLN* 2.8 32.9 + - + +
649A SER* 3.3 7.6 - - - -
650A ARG* 3.0 43.6 + - + +
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Residues in contact with LYS 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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615A PHE* 4.1 32.8 - - + -
631A LEU* 3.6 2.7 - - - +
632A GLN* 1.3 94.4 + - + +
634A LEU* 1.3 81.7 + - - +
646A ARG 3.8 0.9 - - - +
648A GLN* 3.3 34.8 + - - +
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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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609A LEU* 3.9 42.8 - - + +
615A PHE* 4.1 21.5 - - + -
618A ILE* 4.7 8.3 - - + -
631A LEU* 4.1 11.2 - - + -
633A LYS* 1.3 97.9 - - - +
635A HIS* 1.3 61.6 + - - +
636A THR* 4.1 6.3 + - + +
645A ILE* 4.0 16.6 - - + -
646A ARG 3.5 6.5 - - - +
647A PHE* 3.8 30.5 - - + -
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Residues in contact with HIS 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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634A LEU* 1.3 75.4 - - - +
636A THR* 1.3 72.4 + - - +
645A ILE* 3.8 0.3 - - - -
646A ARG* 2.9 48.3 + - + +
687A TYR* 2.9 34.1 + - - -
696A ILE* 4.3 2.0 - - - +
700A GLU* 3.2 19.6 + - + +
699D ILE* 3.1 26.0 + - + -
700D GLU* 2.8 30.3 + - - -
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Residues in contact with THR 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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606A LYS* 2.8 49.4 + - + +
609A LEU* 4.2 24.2 - - + -
610A GLU* 3.5 7.6 + - + +
634A LEU* 4.1 7.1 - - + -
635A HIS* 1.3 95.8 + - - +
637A SER* 1.3 62.6 + - - +
643A LEU* 3.9 11.2 - - + -
644A TYR 3.3 6.3 - - - +
645A ILE* 4.1 22.4 - - + -
699D ILE 5.3 0.3 - - - +
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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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606A LYS* 5.3 1.1 - - - +
635A HIS* 5.0 0.7 - - - -
636A THR* 1.3 73.7 - - - +
638A ILE* 1.3 63.4 + - - +
643A LEU* 3.6 2.5 - - - +
644A TYR* 2.7 43.5 + - - +
687A TYR* 3.1 34.9 - - - -
742B MET* 3.4 28.9 + - - +
698D TRP 5.6 1.6 + - - -
699D ILE* 5.4 3.8 + - - -
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Residues in contact with ILE 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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602A SER* 3.3 48.9 - - - +
603A ALA* 3.7 4.0 - - - +
606A LYS* 3.9 25.7 - - + +
637A SER* 1.3 74.8 + - - +
639A ALA* 1.3 61.8 + - - +
640A GLY 3.4 19.3 - - - +
642A ASN 3.6 5.6 - - - +
643A LEU* 4.1 8.3 - - + -
742B MET* 3.5 15.8 - - - +
584D LEU* 3.8 26.6 - - + +
707D VAL* 4.2 9.9 - - + -
796D THR* 3.3 20.8 - - + +
798D PRO* 6.0 0.2 - - - +
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Residues in contact with ALA 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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637A SER 4.3 0.2 + - - -
638A ILE* 1.3 74.3 - - - +
640A GLY* 1.3 64.6 + - - +
641A ARG 3.1 1.0 + - - -
642A ASN* 3.0 25.7 + - + +
644A TYR* 4.0 13.2 - - + -
738B VAL* 3.9 27.8 - - + -
742B MET* 4.1 12.3 - - - -
778D ILE* 4.5 4.0 - - + -
780D LEU* 3.7 19.3 - - + +
796D THR* 3.6 7.9 - - - -
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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