Contacts of the strand formed by residues 836 - 844 (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 GLY 836 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786C GLU* 3.8 5.8 - - - +
787C VAL* 3.1 35.3 + - - +
835C SER* 1.3 77.5 - - - +
837C LYS* 1.3 66.6 + - - -
864C VAL* 3.8 6.3 - - - -
865C ALA 3.3 13.2 - - - -
866C GLN* 4.4 2.2 - - - -
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Residues in contact with LYS 837 (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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61A HIS* 5.1 11.9 - - + -
62A GLU* 6.2 0.7 - - + +
63A PHE* 4.8 17.7 - - + -
151A GLN* 4.0 12.3 + - - -
152A ASN* 3.0 41.8 + - - +
159A ILE 5.6 0.2 + - - -
161A ARG 4.7 2.2 + - - -
162A ILE* 5.7 3.8 - - - +
163A PRO* 4.7 7.7 - - - +
784C GLY 3.8 23.3 + - - +
785C ALA 3.5 1.6 - - - -
786C GLU* 3.5 25.3 + - + +
836C GLY* 1.3 75.0 - - - -
838C VAL* 1.3 67.0 + - - +
839C ILE* 5.2 0.4 - - + -
864C VAL* 3.2 4.4 - - - +
865C ALA* 2.9 33.8 + - - +
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Residues in contact with VAL 838 (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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61A HIS* 3.7 5.4 - - - -
781C VAL* 3.7 30.1 - - + -
782C ARG 4.0 11.4 - - - +
783C ILE* 4.5 0.4 - - - -
784C GLY* 3.0 27.3 + - - +
785C ALA 3.1 18.8 + - - +
787C VAL* 3.9 12.1 - - + -
793C LEU* 4.6 0.2 - - + -
837C LYS* 1.3 72.8 - - - +
839C ILE* 1.3 62.6 + - - +
841C ILE* 3.5 32.3 - - + -
862C VAL* 3.5 22.2 - - + -
863C TYR 3.6 4.3 - - - +
864C VAL* 4.4 7.2 - - + +
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Residues in contact with ILE 839 (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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61A HIS* 3.4 19.1 + - + +
63A PHE* 3.9 31.6 - - + +
666C PHE* 4.6 12.1 - - + +
743C ILE* 4.2 22.9 - - + -
783C ILE* 3.1 24.0 - - - +
837C LYS* 4.5 1.1 - - + +
838C VAL* 1.3 73.3 - - - +
840C GLY* 1.3 61.1 + - - +
863C TYR* 2.8 20.2 + - + +
865C ALA* 3.2 37.7 - - + +
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Residues in contact with GLY 840 (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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783C ILE* 5.0 1.6 - - - -
838C VAL 3.9 0.2 - - - -
839C ILE* 1.3 85.4 - - - +
841C ILE* 1.3 72.3 + - - +
862C VAL* 3.7 0.7 - - - +
863C TYR* 3.0 39.6 + - - +
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Residues in contact with ILE 841 (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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778C ARG* 4.4 9.4 - - - +
780C ILE* 4.0 17.0 - - + -
781C VAL 3.8 17.5 - - - +
783C ILE* 3.6 30.8 - - + +
838C VAL* 3.5 20.4 - - + -
840C GLY* 1.3 82.6 - - - +
842C ARG* 1.3 67.8 + - - +
843C VAL* 4.2 3.8 + - + +
860C VAL* 3.4 27.4 - - + -
861C ARG 3.5 4.3 - - - +
862C VAL* 4.2 16.4 - - + -
863C TYR* 5.6 0.9 - - - -
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Residues in contact with ARG 842 (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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115C ASP* 3.5 26.1 + - - +
841C ILE* 1.3 76.6 + - - +
843C VAL* 1.3 90.5 + - - +
844C PHE* 3.2 49.2 - - + -
859C LEU* 3.6 2.3 - - + +
860C VAL* 2.9 6.4 - - - +
861C ARG* 2.8 46.1 + - + +
863C TYR* 4.9 11.6 - - + +
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Residues in contact with VAL 843 (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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778C ARG* 3.6 31.4 - - - +
841C ILE* 4.1 4.0 - - + +
842C ARG* 1.3 94.4 + - - +
844C PHE* 1.3 67.3 + - - +
845C SER* 4.2 6.5 + - - +
850C ASP* 4.5 1.2 - - - +
858C GLU* 3.5 28.9 - - + +
859C LEU 3.5 2.0 - - - +
860C VAL* 4.1 8.3 - - + -
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Residues in contact with PHE 844 (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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115C ASP* 3.9 24.2 - - - -
116C LYS* 4.6 13.0 - - + -
117C ASP* 5.8 3.6 - - - -
842C ARG* 3.2 57.4 - - + -
843C VAL* 1.3 74.4 - - - +
845C SER* 1.3 59.8 + - - +
850C ASP* 3.3 20.0 - - + +
852C LEU* 3.6 11.5 - - + +
858C GLU* 3.1 4.1 - - - -
859C LEU* 2.4 87.2 + - + +
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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