Contacts of the strand formed by residues 701 - 708 (chain D) in PDB entry 2C11
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 VAL 701 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488D ARG* 3.8 4.4 - - - -
489D PHE* 3.1 54.8 + - + +
608D LEU* 3.1 25.4 - - - +
610D PHE* 3.7 30.7 - - + -
680D ALA* 4.3 1.6 - - + -
681D GLY 3.8 17.5 - - - +
682D PHE* 3.8 23.1 - - + -
699D ASN 3.3 8.2 + - - +
700D GLY* 1.3 79.2 - - - +
702D GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 702 (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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487D ILE* 3.0 15.0 - - - -
488D ARG* 4.3 0.9 - - - -
489D PHE* 5.5 0.2 - - - -
526D PHE* 5.6 1.8 - - - -
607D MET* 3.9 2.8 - - - +
608D LEU* 3.2 29.5 + - - +
609D SER* 5.6 0.2 - - - -
678D VAL* 4.7 0.5 - - - +
680D ALA* 4.0 17.2 - - - +
701D VAL* 1.3 77.0 - - - +
703D PHE* 1.3 75.2 + - - +
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Residues in contact with PHE 703 (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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363D ILE* 4.8 2.2 - - + -
485D ILE 4.0 0.2 - - - +
486D GLU* 3.6 3.8 - - - +
487D ILE* 2.9 63.5 + - + +
488D ARG* 4.8 0.2 - - - +
526D PHE* 3.8 36.6 - + + -
528D VAL* 4.1 18.6 - - + -
605D ILE* 4.9 3.4 - - + -
606D GLN 3.0 15.5 - - - +
607D MET* 4.0 11.9 - - + +
608D LEU* 4.2 8.7 - - - +
678D VAL* 3.6 31.2 - - + -
680D ALA* 5.4 0.4 - - + -
702D GLY* 1.3 81.9 - - - +
704D PHE* 1.3 68.8 + - - +
705D LEU* 3.9 27.1 - - + -
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Residues in contact with PHE 704 (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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697C VAL* 4.0 27.8 - - + -
698C GLY* 3.8 20.4 - - - -
480D HIS* 4.1 2.0 - + - -
484D ALA* 5.0 1.6 - - + -
485D ILE 3.4 7.0 - - - -
486D GLU* 3.2 48.2 - - + -
488D ARG* 4.4 2.9 - - - -
604D ARG 3.2 4.6 - - - +
605D ILE* 3.4 1.6 - - - -
606D GLN* 2.6 48.3 + - + +
608D LEU* 3.9 31.2 - - + -
703D PHE* 1.3 80.4 - - - +
705D LEU* 1.3 70.7 + - - +
706D ARG* 3.7 23.1 - - + -
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Residues in contact with LEU 705 (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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360D VAL* 4.4 7.6 - - + -
363D ILE* 3.3 34.5 - - + -
484D ALA* 3.1 6.3 - - - -
485D ILE* 2.8 58.5 + - + +
487D ILE* 5.3 0.2 - - + -
528D VAL* 4.1 14.4 - - + -
530D LEU* 4.4 11.2 - - + -
603D TYR* 3.4 18.4 - - + -
604D ARG 3.4 4.0 - - - +
605D ILE* 4.3 18.4 - - + -
678D VAL* 6.4 0.2 - - + -
703D PHE* 3.9 22.2 - - + -
704D PHE* 1.3 84.8 - - - +
706D ARG* 1.3 59.3 + - - +
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Residues in contact with ARG 706 (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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687C HIS* 4.8 4.0 + - + -
697C VAL* 3.1 21.8 + - - -
698C GLY 3.5 1.6 + - - -
699C ASN* 2.8 29.3 + - - +
1747C CU 3.1 25.5 - - - -
484D ALA* 4.2 8.5 - - + -
586D TYR* 4.5 0.6 + - - -
603D TYR* 3.3 5.3 - - - -
604D ARG* 2.6 78.0 + - + +
606D GLN* 3.3 30.9 + - + -
704D PHE* 3.7 22.0 - - + -
705D LEU* 1.3 76.3 - - - +
707D PRO* 1.3 72.9 - - + +
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Residues in contact with PRO 707 (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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687C HIS* 3.5 20.3 + - + -
689C GLU* 3.4 32.1 - - + +
482D SER* 3.8 16.4 - - - +
483D GLY 4.1 6.5 - - - +
484D ALA* 4.2 8.7 - - + +
602D GLY 3.9 1.1 - - - +
603D TYR* 3.3 36.8 - - + +
604D ARG* 5.5 0.2 - - - +
706D ARG* 1.3 88.7 - - + +
708D TYR* 1.3 59.6 + - - +
710D PHE* 3.8 1.3 - - + -
711D PHE* 3.6 12.3 - - + -
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Residues in contact with TYR 708 (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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509C ASN* 2.9 22.1 + - - -
685C ILE* 3.0 31.1 - - - +
687C HIS* 3.6 20.0 - + - -
689C GLU* 3.7 1.3 - - - -
542D GLU* 2.5 37.1 + - - -
586D TYR* 3.4 28.9 - + - -
588D TYR* 3.9 28.3 - + + -
600D PRO 3.8 1.1 - - - +
602D GLY 2.9 32.0 + - - +
604D ARG* 4.4 15.5 - - + +
706D ARG 3.5 0.2 + - - -
707D PRO* 1.3 74.0 - - - +
709D ASN* 1.3 90.9 + - - +
710D PHE 3.0 2.9 + - - -
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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