Contacts of the strand formed by residues 740 - 751 (chain C) in PDB entry 6VVT
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 740 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607C VAL* 3.6 16.2 - - - +
608C PRO 3.2 23.8 - - - -
609C LEU* 3.9 4.0 - - - -
610C VAL* 4.4 2.5 - - - -
738C LEU 3.8 0.4 + - - -
739C THR* 1.3 75.0 - - - +
741C ILE* 1.3 63.2 + - - +
742C HIS* 2.8 27.4 + - - -
868C ARG* 3.0 31.8 + - - +
1023C LYS* 2.9 21.0 + - - -
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Residues in contact with ILE 741 (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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63A PHE* 3.3 44.4 - - + -
74A THR* 4.3 8.7 - - + +
608C PRO* 4.3 6.4 + - - +
610C VAL* 3.5 27.7 - - + +
666C PHE* 3.8 16.8 - - + -
674C CYS* 3.5 39.4 + - + +
676C ASN* 6.4 0.2 - - + -
740C SER* 1.3 75.3 - - - +
742C HIS* 1.3 75.1 + - - +
743C ILE* 4.5 1.8 - - + -
865C ALA* 4.4 10.1 - - + -
866C GLN 3.2 11.7 - - - +
867C LYS* 4.6 8.7 - - + +
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Residues in contact with HIS 742 (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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607C VAL* 4.3 21.0 - - + +
608C PRO* 5.8 0.7 - - + -
671C HIS 5.3 0.4 + - - -
672C GLY* 3.1 14.8 + - - +
673C THR* 4.3 13.7 - - + +
740C SER* 2.8 32.3 + - - -
741C ILE* 1.3 78.3 + - - +
743C ILE* 1.3 63.1 + - - +
744C GLU* 5.4 2.9 - - - +
865C ALA* 3.4 1.2 - - - -
866C GLN* 2.8 46.3 + - + +
868C ARG* 3.3 52.2 + - + +
1025C HIS* 4.9 7.0 + + - -
1027C LEU* 3.4 23.0 - - + +
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Residues in contact with ILE 743 (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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666C PHE* 3.3 31.4 - - + +
668C ARG* 3.2 42.9 + - + +
672C GLY* 2.7 34.8 + - - +
674C CYS* 4.0 22.7 - - + -
741C ILE* 4.5 2.2 - - + -
742C HIS* 1.3 75.6 - - - +
744C GLU* 1.3 72.6 + - - +
839C ILE* 4.2 13.0 - - + -
863C TYR* 4.4 13.5 - - + -
864C VAL 3.2 13.0 - - - +
865C ALA* 4.1 12.6 - - + -
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Residues in contact with GLU 744 (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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668C ARG* 3.8 15.5 + - - +
671C HIS 5.6 0.7 - - - +
672C GLY* 4.7 4.4 - - - -
742C HIS* 5.4 3.1 - - - +
743C ILE* 1.3 82.7 - - - +
745C GLU* 1.3 64.7 + - - +
746C HIS* 3.8 13.9 + - + +
834C GLU* 3.3 31.0 - - - +
862C VAL 3.8 0.3 - - - +
863C TYR* 3.3 5.0 - - - +
864C VAL 2.5 42.9 + - - +
866C GLN* 4.4 9.5 - - - +
868C ARG* 5.5 2.6 + - - -
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Residues in contact with GLU 745 (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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668C ARG* 3.5 30.8 + - - +
744C GLU* 1.3 78.2 - - - +
746C HIS* 1.3 78.0 + - - +
747C GLU* 4.3 20.6 - - + +
861C ARG* 4.3 4.2 - - + +
862C VAL 3.7 2.9 - - - +
863C TYR* 3.2 44.0 + - + -
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Residues in contact with HIS 746 (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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744C GLU* 3.8 21.1 + - + +
745C GLU* 1.3 77.6 - - - +
747C GLU* 1.3 60.5 + - - +
793C LEU* 4.0 19.0 - - + +
828C LEU* 4.0 20.9 - - + -
829C LYS 5.0 3.4 - - - -
830C VAL* 6.0 0.7 - - + -
831C PRO* 3.3 37.5 - - + +
834C GLU* 3.3 24.7 + - - -
861C ARG* 3.1 8.0 - - - +
862C VAL* 2.8 41.3 + - + +
864C VAL* 4.3 16.1 - - + +
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Residues in contact with GLU 747 (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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117C ASP* 4.3 14.0 - - - +
745C GLU* 4.3 14.2 - - + +
746C HIS* 1.3 75.2 - - - +
748C ILE* 1.3 67.3 + - - +
828C LEU* 3.5 13.9 - - - +
859C LEU* 3.8 28.3 - - + +
860C VAL 3.7 7.0 - - - +
861C ARG* 3.6 22.5 - - + +
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Residues in contact with ILE 748 (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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747C GLU* 1.3 79.2 - - - +
749C ASP* 1.3 77.0 + - - +
760C ILE* 5.7 2.9 - - + -
794C VAL* 3.6 22.0 - - + -
796C LYS* 3.9 31.4 - - + +
826C THR* 5.5 3.4 - - - +
827C SER 6.0 0.4 - - - -
828C LEU* 3.9 24.2 - - + +
859C LEU* 3.0 19.2 - - - +
860C VAL* 3.1 38.4 + - + +
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Residues in contact with ASP 749 (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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748C ILE* 1.3 88.2 - - - +
750C ALA* 1.3 53.6 - - - +
751C ARG* 3.0 44.6 + - + +
796C LYS* 2.2 46.6 + - - +
856C VAL* 4.4 5.4 - - + -
858C GLU 3.7 5.2 - - - -
859C LEU* 4.2 11.2 - - + -
332D GLY* 4.3 9.6 + - - -
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Residues in contact with ALA 750 (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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749C ASP* 1.3 73.5 - - - +
751C ARG* 1.3 52.8 - - - +
758C GLU* 3.8 28.3 - - + +
760C ILE* 4.5 18.4 - - + +
796C LYS* 4.8 1.3 - - - -
856C VAL* 3.2 1.9 - - - +
857C ASN* 2.3 39.2 + - + -
858C GLU* 2.9 29.4 + - + +
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Residues in contact with ARG 751 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C ASP* 3.0 35.8 + - + +
750C ALA* 1.3 78.9 - - - +
752C ASP* 1.3 65.4 + - - +
753C THR* 3.9 4.3 + - + +
757C ALA* 4.4 0.9 - - - -
758C GLU* 2.7 35.5 + - - +
796C LYS* 4.7 1.7 - - - +
853C PRO* 5.0 11.6 - - - +
854C ALA 5.2 4.1 + - - -
855C GLY* 2.9 15.7 - - - +
856C VAL* 3.2 35.0 - - + +
857C ASN* 4.0 4.9 - - - +
332D GLY* 2.2 42.5 + - - -
333D GLY* 4.3 5.9 - - - +
356F ARG* 4.5 8.7 - - - +
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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