Contacts of the strand formed by residues 630 - 636 (chain C) 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 TYR 630 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C HIS* 5.9 0.9 - - - +
576C ALA* 4.9 6.1 - - + -
577C PHE 3.5 9.9 - - - +
578C LEU* 3.2 33.9 - - + -
579C VAL* 3.4 10.6 - - - +
626C SER 4.0 11.4 - - - -
627C TRP 2.9 10.6 + - - +
628C GLU 3.1 0.6 - - - -
629C ARG* 1.3 117.8 + - - +
631C GLN* 1.3 59.5 + - - +
632C LEU* 4.0 14.1 - - - +
633C ALA* 4.6 3.4 - - + -
660C PHE* 3.8 28.0 - + + -
661C SER* 4.1 11.9 + - - -
664C ILE* 3.2 33.9 - - + +
677C TRP 5.5 1.1 - - - +
679C THR* 2.9 29.8 - - - +
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Residues in contact with GLN 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C PHE* 2.7 10.9 + - + +
578C LEU 2.5 23.1 + - - +
579C VAL* 3.5 19.5 - - + -
580C GLY 3.6 4.5 - - - +
581C SER* 2.7 34.6 + - - +
583C THR* 3.5 21.9 + - + +
607C MET* 3.5 30.9 - - + +
611C ALA* 6.3 1.6 - - + -
630C TYR* 1.3 75.0 - - - +
632C LEU* 1.3 65.7 + - + +
677C TRP 4.3 0.4 - - - -
678C VAL* 3.4 2.4 - - - -
679C THR* 2.8 30.4 + - - +
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Residues in contact with LEU 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C ALA 4.1 3.6 - - - +
576C ALA* 3.5 0.2 - - - -
577C PHE* 2.6 41.1 + - + +
583C THR* 6.3 0.7 - - + -
587C LEU* 4.2 26.7 - - + -
605C ILE* 4.5 24.7 - - + +
607C MET* 4.2 11.9 - - - -
630C TYR* 4.0 4.4 - - - +
631C GLN* 1.3 85.1 - - + +
633C ALA* 1.3 72.7 + - - +
634C VAL* 4.5 8.3 - - + -
676C ALA* 3.9 8.7 - - + -
677C TRP 3.1 31.2 - - - +
678C VAL* 3.6 15.9 - - + -
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Residues in contact with ALA 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C ALA 3.5 8.3 - - - -
576C ALA* 3.7 15.7 - - + +
630C TYR* 4.6 10.5 - - + -
632C LEU* 1.3 79.1 - - - +
634C VAL* 1.3 68.8 + - - +
635C THR* 5.3 1.1 - - + -
660C PHE* 4.6 5.6 - - + -
664C ILE* 4.4 15.7 - - + -
676C ALA* 3.3 0.3 - - - -
677C TRP* 2.7 44.5 + - + +
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Residues in contact with VAL 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C VAL* 4.3 13.2 - - + -
572C GLU* 3.8 22.4 + - - +
575C ALA* 3.6 30.6 + - + +
576C ALA* 4.7 0.4 - - - +
587C LEU* 6.3 1.6 - - + -
589C LEU* 4.2 21.8 - - + -
605C ILE* 5.9 0.4 - - + -
632C LEU* 4.5 10.5 - - + -
633C ALA* 1.3 84.5 - - - +
635C THR* 1.3 71.7 + - - +
669C ILE* 4.0 4.2 - - + +
674C LEU* 4.1 22.4 - - + -
675C VAL 3.4 13.9 - - - +
676C ALA* 4.3 10.5 - - + -
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Residues in contact with THR 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C GLU* 3.7 15.9 - - + +
633C ALA* 5.1 1.6 - - + -
634C VAL* 1.3 84.8 - - - +
636C GLN* 1.3 67.1 + - - +
641C GLU* 4.1 8.2 + - - -
660C PHE* 5.6 0.4 - - + -
663C PHE* 3.5 31.6 - - + +
664C ILE* 4.6 9.6 - - + -
669C ILE* 4.5 0.9 - - - -
674C LEU* 3.0 12.9 - - - +
675C VAL* 2.9 39.0 + - - +
677C TRP* 3.3 27.1 + - + +
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Residues in contact with GLN 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C GLU* 3.3 8.1 + - - +
635C THR* 1.3 79.6 + - - +
637C ARG* 1.3 53.6 + - - +
638C LYS* 2.6 43.1 + - + +
641C GLU* 4.0 2.4 - - - +
667C GLU* 2.7 42.7 + - - +
668C THR* 3.0 27.5 + - - +
669C ILE* 4.9 0.9 - - + -
672C LYS* 3.9 22.1 - - + +
673C ASP 3.4 7.4 - - - +
674C LEU* 4.0 9.2 - - + -
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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