Contacts of the helix formed by residues 702 - 722 (chain C) in PDB entry 4OQB
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 SER 702 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C GLU* 3.0 39.9 + - - +
643C ILE 5.1 3.4 - - - -
644C ASP* 5.2 7.0 - - - +
700C LYS 3.7 1.5 + - - -
701C LEU* 1.3 79.7 - - - +
703C LYS* 1.3 68.3 + - - +
704C ARG* 3.4 16.5 + - - +
705C GLN* 3.5 8.2 + - - +
706C ILE* 3.2 27.5 + - - +
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Residues in contact with LYS 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701C LEU 5.8 0.7 - - - +
702C SER* 1.3 77.6 + - - +
704C ARG* 1.3 64.4 + - + +
705C GLN 3.2 0.2 - - - -
706C ILE* 3.4 6.9 + - + +
707C GLN* 3.1 42.4 + - - +
769C LEU* 3.8 40.4 - - + +
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Residues in contact with ARG 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C GLU* 6.3 2.7 - - + -
702C SER* 3.4 9.1 + - - +
703C LYS* 1.3 78.0 - - + +
705C GLN* 1.3 63.0 + - - +
707C GLN* 3.7 16.1 + - - +
708C ALA* 3.3 21.3 + - - +
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Residues in contact with GLN 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639C TYR* 4.3 1.2 + - - -
641C LEU* 3.7 26.1 - - - +
642C GLU* 2.9 29.8 - - + +
701C LEU* 3.7 29.2 - - + +
702C SER* 3.5 25.7 + - - +
704C ARG* 1.3 77.3 - - - +
706C ILE* 1.3 60.0 + - - +
708C ALA* 3.1 8.9 + - - +
709C ALA* 2.9 23.2 + - - +
739C LEU* 3.0 50.3 + - + +
740C ILE* 5.7 0.7 - - + -
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Residues in contact with ILE 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701C LEU* 3.9 31.9 - - + +
702C SER 3.2 20.5 + - - +
703C LYS* 3.4 9.2 + - + +
705C GLN* 1.3 76.7 - - - +
707C GLN* 1.3 56.6 + - + +
709C ALA* 3.2 7.4 + - - +
710C TYR* 2.8 50.0 + - + -
740C ILE* 5.6 2.2 - - + -
765C LEU* 4.4 15.9 - - + +
768C LEU* 4.2 18.8 - - + -
769C LEU* 3.7 30.5 - - + -
772C GLU* 6.0 3.6 - - + -
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Residues in contact with GLN 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703C LYS* 3.1 35.0 + - + +
704C ARG* 3.8 16.1 - - - +
706C ILE* 1.3 77.0 - - - +
708C ALA* 1.3 55.9 + - - +
710C TYR* 3.4 13.1 + - + +
711C SER* 2.9 31.1 + - - -
883C GLU* 3.8 35.3 + - + +
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Residues in contact with ALA 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C ARG 3.3 10.5 + - - +
705C GLN* 3.1 11.5 + - - +
707C GLN* 1.3 76.0 - - - +
709C ALA* 1.3 60.3 + - - +
711C SER* 3.2 10.2 + - - -
712C ILE* 2.9 34.3 + - + +
735C ARG* 5.5 6.1 - - - +
739C LEU* 3.8 14.6 - - + -
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Residues in contact with ALA 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705C GLN 2.9 12.5 + - - +
706C ILE* 3.4 10.5 - - - +
708C ALA* 1.3 74.5 - - - +
710C TYR* 1.3 62.2 + - - +
712C ILE* 3.5 4.7 + - - -
713C LEU* 3.2 26.0 + - - +
736C PHE* 3.6 10.7 - - + -
739C LEU* 3.4 11.1 - - + +
740C ILE* 3.4 38.1 - - + -
765C LEU* 3.9 6.1 - - + -
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Residues in contact with TYR 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706C ILE* 2.8 43.1 + - + -
707C GLN* 3.4 13.0 - - + +
709C ALA* 1.3 76.2 - - - +
711C SER* 1.3 56.3 + - - +
713C LEU* 3.2 7.9 + - + +
714C SER* 3.0 24.6 + - - -
762C VAL* 4.2 7.9 - - + -
765C LEU* 3.4 26.4 + - + +
766C ASP* 2.7 41.5 + - - -
769C LEU* 5.1 6.9 - - + +
881C PRO* 4.2 19.2 - - + +
883C GLU* 3.5 22.1 - - + +
884C ALA* 3.4 31.0 - - + -
885C PRO* 4.0 10.7 - - + +
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Residues in contact with SER 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707C GLN 2.9 19.3 + - - -
708C ALA* 3.2 12.3 + - - -
710C TYR* 1.3 76.4 - - - +
712C ILE* 1.3 58.5 + - - +
714C SER* 2.6 23.5 + - - -
715C GLU* 2.9 26.9 + - - +
883C GLU* 3.9 17.4 + - - +
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Residues in contact with ILE 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C ALA* 2.9 21.4 + - + +
709C ALA* 3.7 5.8 - - - +
710C TYR 3.3 0.2 - - - -
711C SER* 1.3 75.3 - - - +
713C LEU* 1.3 62.8 + - - +
715C GLU* 3.2 12.6 + - - +
716C VAL* 3.0 24.5 + - + +
732C LEU* 3.2 41.3 - - + +
735C ARG* 3.8 50.9 - - + +
736C PHE* 3.9 15.0 - - + +
739C LEU* 3.8 22.7 - - + -
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Residues in contact with LEU 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C ALA 3.2 3.1 + - - +
710C TYR* 3.2 9.7 + - + +
712C ILE* 1.3 79.1 - - - +
714C SER* 1.3 61.5 + - - +
716C VAL* 3.1 15.1 + - + +
717C GLN 3.2 10.2 + - - -
736C PHE* 3.4 36.3 - - + -
752C LEU* 4.0 17.0 - - + -
758C VAL* 3.5 27.9 - - + +
761C LYS* 3.5 23.1 - - + +
762C VAL* 3.5 36.3 - - + +
765C LEU* 4.1 10.3 - - + -
885C PRO* 4.3 7.0 - - + -
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Residues in contact with SER 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710C TYR 3.0 4.8 + - - -
711C SER* 2.6 28.2 + - - -
713C LEU* 1.3 76.4 - - - +
715C GLU* 1.3 60.4 + - - +
717C GLN* 3.7 7.1 + - - +
718C GLN* 3.3 21.7 + - - +
883C GLU 3.6 18.4 + - - -
884C ALA 4.4 1.3 - - - -
885C PRO* 4.0 23.5 - - - +
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Residues in contact with GLU 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711C SER* 2.9 25.6 + - - +
712C ILE* 3.2 12.3 + - - +
714C SER* 1.3 77.5 + - - +
716C VAL* 1.3 58.8 - - - +
718C GLN* 3.5 16.9 + - - +
719C ALA* 2.9 27.5 + - - +
728C GLN* 5.0 6.5 + - - +
732C LEU* 3.5 28.5 - - + +
735C ARG* 5.1 8.1 + - - -
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Residues in contact with VAL 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C ILE* 3.0 23.5 + - + +
713C LEU* 3.1 10.0 + - - +
715C GLU* 1.3 74.1 - - - +
717C GLN* 1.3 54.6 + - - +
719C ALA* 3.0 3.8 + - + +
720C VAL* 2.7 43.1 + - + +
729C ILE* 5.4 2.9 - - + +
732C LEU* 3.4 31.2 - - + -
733C SER* 4.9 0.9 - - - +
752C LEU* 3.1 51.1 - - + +
758C VAL* 4.8 11.7 - - + -
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Residues in contact with GLN 717 (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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713C LEU 3.2 10.1 + - - +
714C SER* 3.9 11.6 - - - +
716C VAL* 1.3 78.8 - - - +
718C GLN* 1.3 76.1 + - - +
720C VAL* 3.7 7.7 - - + +
721C SER* 2.8 38.7 + - - -
755C ALA* 6.3 1.8 - - + +
758C VAL* 4.5 11.8 - - + +
885C PRO* 5.0 1.8 - - + -
886C VAL* 3.6 30.2 - - - +
887C THR* 3.2 31.1 + - + +
937C HIS* 5.5 4.2 + - - -
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Residues in contact with GLN 718 (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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714C SER 3.3 11.4 + - - +
715C GLU* 3.6 19.3 + - - +
716C VAL 3.2 0.2 - - - -
717C GLN* 1.3 87.6 + - - +
719C ALA* 1.3 60.8 + - - +
721C SER* 2.7 21.0 + - - +
722C GLN* 3.4 32.4 + - - +
728C GLN* 5.0 10.1 - - - +
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Residues in contact with ALA 719 (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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715C GLU 2.9 17.9 + - - +
716C VAL* 3.0 8.5 + - - +
718C GLN* 1.3 78.3 - - - +
720C VAL* 1.3 60.8 + - - +
722C GLN* 5.0 0.4 - - - +
723C GLY 3.4 2.4 + - - -
724C SER* 2.8 51.4 + - - -
728C GLN* 3.9 20.4 - - + +
729C ILE* 4.3 13.1 - - + +
732C LEU* 4.3 4.5 - - + -
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Residues in contact with VAL 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C VAL* 2.7 36.7 + - + +
717C GLN* 3.8 7.6 - - + +
719C ALA* 1.3 72.6 - - - +
721C SER* 1.3 66.3 + - - +
723C GLY* 3.4 11.2 + - - -
729C ILE* 4.6 11.7 - - + -
752C LEU 4.3 0.7 - - - +
753C ASN* 3.3 36.3 - - - +
754C ASN 4.0 14.6 - - - +
755C ALA* 4.5 11.0 - - + +
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Residues in contact with SER 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717C GLN* 2.8 26.5 + - - -
718C GLN* 2.7 27.4 + - - +
720C VAL* 1.3 77.3 - - - +
722C GLN* 1.3 60.3 + - - +
723C GLY 3.6 1.9 + - - -
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Residues in contact with GLN 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718C GLN* 3.4 42.9 + - - +
719C ALA* 5.0 0.2 - - - +
720C VAL 3.4 0.2 - - - -
721C SER* 1.3 79.8 + - - +
723C GLY* 1.3 66.1 + - - +
724C SER* 3.4 14.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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