Contacts of the strand formed by residues 630 - 636 (chain D) in PDB entry 2C10
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 TYR 630 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D HIS* 6.0 0.9 - - - +
576D ALA* 3.8 22.9 - - + -
577D PHE 3.3 13.5 - - - +
578D LEU* 3.6 20.0 - - + -
579D VAL* 3.8 6.2 - - - +
626D SER 3.6 20.4 - - - -
627D TRP* 3.5 4.4 - - - +
628D GLU 3.2 0.6 - - - -
629D ARG* 1.3 106.7 + - + +
631D GLN* 1.3 56.3 + - - +
632D LEU 4.0 12.8 - - - +
633D ALA* 4.9 0.4 - - + -
660D PHE* 4.1 22.2 - + + -
661D SER* 4.4 15.0 + - - -
664D ILE* 3.6 33.7 - - + +
677D TRP 5.8 0.4 - - - +
679D THR* 2.6 34.2 + - - +
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Residues in contact with GLN 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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577D PHE 2.7 11.5 + - - +
578D LEU 3.0 21.3 + - - +
579D VAL* 3.8 16.3 - - + +
580D GLY 4.0 3.4 - - - +
581D SER* 2.9 30.1 + - - +
583D THR* 3.5 23.2 + - + +
607D MET* 3.6 31.4 - - + +
609D SER* 6.2 1.9 - - - -
611D ALA* 5.8 4.0 - - + -
630D TYR* 1.3 73.3 - - - +
632D LEU* 1.3 59.1 + - + +
677D TRP 4.4 0.2 - - - -
678D VAL* 3.6 1.7 - - - -
679D THR* 3.0 30.6 + - - +
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Residues in contact with LEU 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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575D ALA 3.5 2.3 - - - +
576D ALA* 3.6 0.2 - - - -
577D PHE* 2.8 51.7 + - + +
583D THR* 5.8 2.0 - - - -
587D LEU* 3.2 35.0 - - + -
605D ILE* 4.3 16.8 - - + +
607D MET* 3.9 20.6 - - + -
630D TYR* 3.3 6.4 - - - +
631D GLN* 1.3 82.2 - - + +
633D ALA* 1.3 67.7 - - - +
634D VAL* 4.8 3.4 - - + -
676D ALA* 4.3 14.8 - - + -
677D TRP 3.2 15.3 - - - +
678D VAL* 3.9 20.4 - - + -
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Residues in contact with ALA 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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575D ALA 3.3 7.4 - - - +
576D ALA* 4.5 3.6 - - + -
630D TYR* 4.9 3.1 - - + -
632D LEU* 1.3 76.5 - - - +
634D VAL* 1.3 64.2 + - - +
635D THR* 4.1 1.3 - - + -
660D PHE* 4.0 21.3 - - + -
664D ILE* 3.9 31.2 - - + -
676D ALA* 3.4 2.1 - - - +
677D TRP* 2.7 42.1 + - + +
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Residues in contact with VAL 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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539D VAL* 3.8 24.7 - - + -
572D GLU* 3.5 23.9 + - - +
575D ALA* 3.4 26.8 + - + +
587D LEU* 4.9 4.9 - - + -
589D LEU* 4.0 20.9 - - + -
632D LEU* 4.8 9.9 - - + -
633D ALA* 1.3 78.8 - - - +
635D THR* 1.3 64.6 + - - +
664D ILE* 5.9 0.2 - - - +
669D ILE* 3.7 6.1 - - + +
674D LEU* 3.9 25.8 - - + -
675D VAL 3.4 10.3 - - - +
676D ALA* 4.3 10.3 - - + -
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Residues in contact with THR 635 (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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572D GLU* 3.4 14.8 - - - +
633D ALA* 4.9 1.1 - - + -
634D VAL* 1.3 79.3 - - - +
636D GLN* 1.3 71.1 + - - +
641D GLU* 4.6 2.5 + - - -
660D PHE* 5.2 0.4 - - + -
663D PHE* 3.9 27.0 - - + +
664D ILE* 4.1 21.3 - - + -
669D ILE* 4.2 0.9 - - - -
674D LEU* 3.3 13.6 - - - +
675D VAL* 2.9 31.5 + - - +
677D TRP* 3.0 33.8 + - + +
1778D CA 4.7 0.4 - - - -
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Residues in contact with GLN 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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572D GLU* 3.0 12.8 + - - +
635D THR* 1.3 86.0 + - - +
637D ARG* 1.3 67.2 + - - +
638D LYS* 3.4 15.9 + - + +
641D GLU* 3.7 11.6 - - - +
667D GLU* 3.9 24.1 - - - +
668D THR* 2.6 45.7 + - - +
669D ILE* 4.4 1.5 - - + +
672D LYS* 3.6 31.0 - - + +
673D ASP 3.5 8.3 - - - +
674D LEU* 4.5 0.9 - - - -
675D VAL* 4.0 0.6 - - - +
677D TRP* 5.8 0.2 - - - -
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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