Contacts of the strand formed by residues 856 - 868 (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 VAL 856 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749C ASP* 4.4 5.6 - - + -
750C ALA 3.3 12.8 - - - +
751C ARG* 3.2 42.0 - - + +
846C ARG* 2.8 30.3 + - - -
852C LEU* 3.5 30.8 - - + +
853C PRO* 2.9 33.5 + - + +
854C ALA 4.4 1.1 - - - +
855C GLY* 1.3 74.4 - - - +
857C ASN* 1.3 62.7 + - - +
858C GLU 3.9 9.9 - - - +
859C LEU* 4.6 4.0 - - + -
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Residues in contact with ASN 857 (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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750C ALA* 2.3 28.4 + - + +
751C ARG 4.5 2.4 - - - -
752C ASP* 4.8 1.2 - - - +
757C ALA* 4.1 23.0 - - - +
758C GLU 4.1 11.1 + - - +
845C SER 3.1 3.1 - - - -
846C ARG* 2.7 55.8 + - + +
852C LEU* 3.8 4.8 - - - +
855C GLY 3.5 13.7 + - - +
856C VAL* 1.3 71.6 - - - +
858C GLU* 1.3 56.0 + - + +
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Residues in contact with GLU 858 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C ASP* 3.7 1.7 - - - -
750C ALA* 2.9 39.0 + - + +
760C ILE* 4.6 22.6 + - + +
778C ARG* 5.2 7.4 + - - +
843C VAL* 3.5 22.6 - - + +
844C PHE 3.1 10.8 - - - +
845C SER* 4.0 16.1 - - - +
852C LEU* 4.0 2.2 - - - -
856C VAL* 3.9 1.6 - - - +
857C ASN* 1.3 81.2 - - + +
859C LEU* 1.3 66.0 + - - +
860C VAL* 5.2 5.5 - - + +
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Residues in contact with LEU 859 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C GLU* 3.8 32.8 - - + +
748C ILE 3.0 24.9 - - - +
749C ASP* 4.2 9.9 - - + -
842C ARG* 3.6 0.8 - - + +
843C VAL* 3.3 0.7 - - - -
844C PHE* 2.4 82.4 + - + +
852C LEU* 3.7 18.8 - - + -
856C VAL* 4.6 3.8 - - + -
858C GLU* 1.3 71.5 - - - +
860C VAL* 1.3 63.1 + - - +
861C ARG* 4.9 2.7 - - + +
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Residues in contact with VAL 860 (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* 3.7 3.1 - - - +
748C ILE* 3.1 48.8 + - + +
778C ARG* 5.6 0.2 - - - +
780C ILE* 4.3 15.5 - - + -
794C VAL* 3.9 23.7 - - + +
841C ILE* 3.4 25.8 - - + -
842C ARG 2.9 15.9 - - - +
843C VAL* 4.1 12.3 - - + -
858C GLU* 5.5 4.9 - - + +
859C LEU* 1.3 75.6 - - - +
861C ARG* 1.3 63.1 + - - +
862C VAL* 4.9 1.1 - - + -
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Residues in contact with ARG 861 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C GLU* 4.3 13.7 - - + +
746C HIS 3.1 14.6 - - - +
747C GLU* 3.6 23.3 - - + +
840C GLY 4.1 0.3 - - - +
841C ILE* 3.5 4.0 - - - +
842C ARG* 2.8 39.1 + - + +
859C LEU* 4.9 2.7 - - + +
860C VAL* 1.3 75.6 - - - +
862C VAL* 1.3 63.0 + - - +
863C TYR* 4.2 9.3 + - + +
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Residues in contact with VAL 862 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744C GLU 3.8 0.5 - - - +
745C GLU* 3.7 1.2 - - - -
746C HIS* 2.8 38.1 + - + +
780C ILE* 5.4 0.7 - - + -
781C VAL* 3.8 18.4 - - + +
793C LEU* 4.6 14.8 - - + -
794C VAL* 3.9 28.9 - - + -
828C LEU* 6.0 0.9 - - + -
838C VAL* 3.5 29.6 - - + -
840C GLY 3.7 4.0 - - - +
841C ILE* 4.2 15.7 - - + -
860C VAL* 4.9 0.7 - - + -
861C ARG* 1.3 75.8 - - - +
863C TYR* 1.3 64.7 + - - +
864C VAL* 4.2 11.9 - - + -
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Residues in contact with TYR 863 (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* 4.3 17.3 - - + -
743C ILE* 4.4 11.0 - - + -
744C GLU 3.3 6.1 - - - +
745C GLU* 3.2 56.2 + - + -
838C VAL* 3.6 4.2 - - - +
839C ILE* 2.8 37.9 + - + -
840C GLY* 3.0 30.0 + - - +
842C ARG* 4.9 12.0 - - + +
861C ARG* 4.4 15.8 - - + +
862C VAL* 1.3 73.4 - - - +
864C VAL* 1.3 57.6 + - - +
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Residues in contact with VAL 864 (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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742C HIS 3.9 0.7 - - - +
743C ILE* 3.2 3.6 - - - -
744C GLU* 2.5 44.9 + - - +
746C HIS* 4.3 23.1 - - + +
787C VAL* 4.2 12.6 - - + -
793C LEU* 4.7 7.4 - - + -
830C VAL* 6.2 0.4 - - + -
834C GLU* 4.7 9.0 - - + +
835C SER 4.7 3.4 - - - +
836C GLY* 3.8 26.2 - - - +
837C LYS 3.2 17.0 - - - +
838C VAL* 4.4 8.5 - - + -
862C VAL* 4.2 16.2 - - + -
863C TYR* 1.3 76.7 - - - +
865C ALA* 1.3 59.9 + - - +
866C GLN* 4.9 2.5 - - + +
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Residues in contact with ALA 865 (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* 3.8 22.1 - - + -
741C ILE* 4.4 3.1 - - + -
742C HIS 3.4 4.7 - - - -
743C ILE* 4.1 10.1 - - + +
836C GLY* 3.3 7.1 - - - -
837C LYS* 2.9 31.5 + - - +
839C ILE* 3.2 35.4 - - + +
864C VAL* 1.3 72.3 - - - +
866C GLN* 1.3 63.5 + - - +
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Residues in contact with GLN 866 (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* 4.8 1.8 - - - -
740C SER 3.8 0.2 - - - +
741C ILE* 3.2 8.6 - - - +
742C HIS* 2.8 46.3 + - + +
744C GLU* 4.4 12.0 - - - +
834C GLU* 3.7 25.9 - - - +
835C SER 3.1 31.0 + - - +
836C GLY* 4.4 1.8 - - - -
864C VAL* 4.9 2.7 - - + +
865C ALA* 1.3 81.6 - - - +
867C LYS* 1.3 62.0 + - - +
868C ARG* 3.1 45.6 + - + +
1029C ASP* 5.1 3.2 + - - +
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Residues in contact with LYS 867 (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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62A GLU* 3.2 33.1 + - - +
63A PHE* 4.7 12.6 - - + -
74A THR* 4.6 5.8 + - - +
77A ILE* 4.8 6.1 - - - +
78A LEU* 3.9 18.3 - - - +
81A LYS* 5.7 0.4 - - - +
165A ASP* 5.1 5.4 + - - +
610C VAL* 4.7 11.4 - - - -
736C ASP* 3.8 24.3 + - - +
739C THR* 3.5 22.7 - - + -
740C SER 4.2 1.8 - - - -
741C ILE* 4.6 11.2 - - + +
866C GLN* 1.3 69.8 - - - +
868C ARG* 1.3 61.4 + - - +
869C LYS* 3.5 11.0 + - - +
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Residues in contact with ARG 868 (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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739C THR* 3.2 6.5 - - - -
740C SER 3.0 35.3 + - - +
742C HIS* 3.3 34.5 + - + +
744C GLU* 5.5 2.8 + - - -
866C GLN* 3.1 43.4 + - + +
867C LYS* 1.3 70.7 - - - +
869C LYS* 1.3 66.9 + - - +
1023C LYS* 3.4 12.6 + - - +
1027C LEU* 3.0 36.1 - - + +
1029C ASP* 3.5 31.2 + - - +
1030C ASP* 3.1 28.5 + - - -
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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