Contacts of the strand formed by residues 629 - 639 (chain D) in PDB entry 1DQA
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 ALA 629 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622D PHE* 3.9 15.9 - - + +
623D ASP* 3.4 13.1 - - - +
625D THR* 5.0 3.4 - - - +
626D SER* 3.0 15.6 + - - -
628D PHE* 1.3 73.0 - - - +
630D ARG* 1.3 80.2 + - - +
631D LEU 4.1 0.7 - - - -
649D SER* 3.6 8.5 - - - +
650D ARG 3.3 9.0 - - - +
659D MET* 3.6 29.9 - - + +
660D ILE* 4.5 3.1 - - + -
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Residues in contact with ARG 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D LYS* 4.2 5.4 - - - +
623D ASP* 3.2 30.3 + - - +
626D SER 2.9 26.9 + - - -
627D ARG* 3.7 20.1 + - - +
628D PHE* 3.1 13.5 + - - +
629D ALA* 1.3 97.3 + - - +
631D LEU* 1.3 61.2 + - - +
632D GLN* 2.8 29.2 + - - +
649D SER* 3.1 6.8 + - - -
650D ARG* 3.1 24.0 + - + -
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Residues in contact with LEU 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D PHE* 3.7 26.9 - - + -
618D ILE* 4.2 9.9 - - + -
619D LYS* 2.8 57.4 + - + +
622D PHE* 3.9 17.0 - - + -
623D ASP* 2.8 19.2 + - - +
629D ALA 4.1 0.2 - - - -
630D ARG* 1.3 69.6 - - - +
632D GLN* 1.3 62.3 + - - +
633D LYS 3.8 4.3 - - - +
634D LEU* 3.8 12.6 - - + -
647D PHE* 4.0 20.0 - - + -
648D GLN 3.4 33.0 - - - +
649D SER* 3.7 4.3 + - - -
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Residues in contact with GLN 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586D ASP 5.0 3.8 - - - +
615D PHE* 3.7 11.8 - - - -
619D LYS* 4.4 3.0 - - - +
630D ARG* 2.8 32.3 + - - +
631D LEU* 1.3 81.8 + - - +
633D LYS* 1.3 66.8 + - + +
648D GLN* 2.7 21.0 + - + +
649D SER* 4.4 0.9 - - - -
650D ARG* 3.8 39.5 + - + +
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Residues in contact with LYS 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D PHE* 3.8 9.6 - - - -
631D LEU* 3.8 1.6 - - - +
632D GLN* 1.3 85.9 - - + +
634D LEU* 1.3 87.0 + - - +
635D HIS* 5.1 8.9 - - - +
646D ARG 3.8 0.4 - - - +
648D GLN* 3.0 55.7 + - + +
700D GLU* 5.4 7.8 + - - -
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Residues in contact with LEU 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D LEU* 4.1 37.5 - - + +
615D PHE* 3.7 25.8 - - + -
618D ILE* 4.5 10.8 - - + -
631D LEU* 3.8 11.7 - - + -
633D LYS* 1.3 97.5 - - - +
635D HIS* 1.3 59.3 + - - +
636D THR* 4.0 8.7 + - + -
645D ILE* 4.1 14.6 - - + -
646D ARG 3.3 3.1 - - - -
647D PHE* 3.5 37.7 - - + -
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Residues in contact with HIS 635 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A LYS* 5.9 4.9 + - - -
699A ILE* 3.1 28.9 + - - +
700A GLU* 4.6 8.5 - - + -
606D LYS* 6.0 0.7 - - - -
633D LYS* 5.1 9.0 - - - +
634D LEU* 1.3 73.7 - - - +
636D THR* 1.3 71.0 + - - +
637D SER* 5.1 1.3 - - - -
646D ARG* 2.7 46.1 + - + +
687D TYR* 3.3 26.8 + - - -
696D ILE* 4.1 4.9 - - + -
700D GLU* 2.9 40.6 + - - +
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Residues in contact with THR 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D LYS* 3.1 39.5 + - - +
609D LEU* 3.6 36.6 - - + -
610D GLU* 3.3 14.8 + - + +
634D LEU* 4.0 10.0 + - + -
635D HIS* 1.3 86.4 + - - +
637D SER* 1.3 61.9 - - - +
643D LEU* 4.1 12.6 - - - -
644D TYR 3.3 6.1 - - - -
645D ILE* 3.8 15.0 - - + -
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Residues in contact with SER 637 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A TRP 5.8 0.2 + - - -
699A ILE 5.2 3.6 - - - -
742C MET* 3.2 27.9 + - - +
606D LYS* 4.3 3.6 - - - +
635D HIS* 4.2 3.8 + - - -
636D THR* 1.3 73.1 - - - +
638D ILE* 1.3 62.8 + - - +
643D LEU* 3.4 1.1 - - - +
644D TYR* 2.7 40.5 + - - +
687D TYR* 3.1 32.8 + - - -
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Residues in contact with ILE 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A LEU* 3.6 36.3 - - + +
707A VAL* 3.7 23.8 - - + -
796A THR* 3.3 18.7 - - + +
742C MET* 3.4 16.1 - - - +
599D ALA 4.6 2.0 - - - +
602D SER* 3.9 18.4 - - - +
603D ALA 4.7 1.3 - - - +
606D LYS* 4.0 17.9 - - + +
637D SER* 1.3 76.4 + - - +
639D ALA* 1.3 60.6 + - - +
640D GLY 3.7 14.8 - - - +
642D ASN 3.3 11.4 - - - +
643D LEU* 3.4 25.8 - - + -
644D TYR* 5.0 0.4 - - - -
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Residues in contact with ALA 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778A ILE* 4.2 6.5 - - + -
780A LEU* 3.5 29.4 - - + +
796A THR* 3.5 9.2 - - - -
738C VAL* 4.0 18.8 - - + -
742C MET* 4.0 14.8 - - - -
638D ILE* 1.3 75.7 - - - +
640D GLY* 1.3 63.1 - - - +
641D ARG 3.3 0.5 + - - -
642D ASN* 3.0 21.5 + - + +
644D TYR* 4.1 8.5 - - + -
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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