Contacts of the strand formed by residues 84 - 89 (chain L) in PDB entry 1VCB
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 84 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78L ASN* 3.3 29.6 - - - +
80L SER* 4.0 1.8 - - - +
82L ARG 3.7 5.6 - - - +
83L VAL* 1.3 72.8 - - - +
85L LEU* 1.3 69.4 + - - +
86L PRO* 3.5 5.0 - - + +
100L THR* 3.3 6.9 - - - -
101L LEU* 2.8 47.0 + - + +
119L PHE* 4.0 28.0 - - + -
120L ARG 3.6 7.6 - - - +
122L ALA* 4.2 1.6 - - - -
128L LEU* 3.6 22.0 - - + -
151L ILE* 3.8 15.0 - - + -
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Residues in contact with LEU 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L VAL* 1.3 73.3 - - - +
86L PRO* 1.4 68.1 - - - +
87L VAL* 3.2 36.0 - - + +
97L PRO* 3.9 20.4 - - + -
98L TYR 3.4 23.6 - - - +
100L THR* 4.1 11.9 - - + -
119L PHE* 3.7 0.3 - - - -
120L ARG* 2.8 40.3 + - + +
121L ASP 4.5 0.7 - - - -
122L ALA* 3.6 26.9 - - + +
125L HIS* 5.2 12.1 - - + +
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Residues in contact with PRO 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L PHE* 3.7 20.9 - - + -
84L VAL* 3.5 11.9 - - + +
85L LEU* 1.4 85.2 - - - +
87L VAL* 1.3 63.7 + - - +
88L TRP 4.2 0.4 - - - -
97L PRO* 3.7 1.6 - - - +
98L TYR* 3.1 42.4 + - + +
99L PRO 3.4 26.9 - - - +
101L LEU* 4.7 5.6 - - + +
107L ARG* 5.5 1.1 - - - +
117L TRP* 4.1 4.5 - - + -
119L PHE* 3.6 32.5 - - + -
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Residues in contact with VAL 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L LEU* 3.2 38.1 - - + +
86L PRO* 1.3 74.4 - - - +
88L TRP* 1.3 63.1 + - - +
89L LEU* 3.9 4.2 + - + +
95L PRO* 3.7 20.0 - - + -
96L GLN 3.5 24.9 - - - +
97L PRO* 4.5 3.4 - - + -
117L TRP* 3.4 6.3 - - - -
118L LEU* 2.7 64.8 + - + +
120L ARG* 4.8 4.5 - - + -
194L VAL* 5.0 5.6 - - + -
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Residues in contact with TRP 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L SER* 2.9 17.6 + - - -
87L VAL* 1.3 73.9 - - - +
89L LEU* 1.3 74.3 + - - +
90L ASN* 4.4 14.1 - - - -
91L PHE* 4.1 24.7 - + - -
95L PRO* 3.6 0.7 - - - +
96L GLN* 2.6 84.5 + - + +
98L TYR* 3.7 17.9 - - + -
115L HIS* 3.0 37.7 + + + -
116L LEU 3.5 11.9 - - - -
117L TRP* 3.6 41.3 - + + -
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Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LEU* 3.8 25.1 - - + +
64L ARG* 4.7 1.8 - - - -
65L SER* 2.4 29.1 + - - -
87L VAL* 4.6 4.5 - - + +
88L TRP* 1.3 77.2 + - - +
90L ASN* 1.3 66.0 + - - +
93L GLY 4.4 4.9 - - - +
94L GLU 3.6 0.7 - - - -
95L PRO* 3.9 20.2 - - + -
116L LEU* 2.8 43.9 + - + +
118L LEU* 4.4 13.0 - - + -
135L LEU* 4.9 7.6 - - + -
198L LEU* 3.8 43.3 - - + -
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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