Contacts of the strand formed by residues 84 - 89 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78F ASN* 3.3 30.5 - - - +
80F SER* 4.0 1.8 - - - +
82F ARG 3.7 5.8 - - - +
83F VAL* 1.3 73.3 - - - +
85F LEU* 1.3 71.0 + - - +
86F PRO* 3.5 4.6 - - + +
100F THR* 3.2 6.9 - - - -
101F LEU* 2.8 46.0 + - + +
119F PHE* 4.0 28.0 - - + -
120F ARG 3.6 7.9 - - - +
122F ALA* 4.2 1.3 - - - -
128F LEU* 3.6 22.4 - - + -
151F ILE* 3.8 14.6 - - + -
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F VAL 3.9 0.6 + - - -
84F VAL* 1.3 73.1 - - - +
86F PRO* 1.3 67.1 - - - +
87F VAL* 3.3 35.2 - - + +
97F PRO* 4.0 20.2 - - + -
98F TYR 3.5 23.8 - - - +
100F THR* 4.0 12.6 - - + -
119F PHE* 3.7 0.3 - - - -
120F ARG* 2.8 39.4 + - + +
121F ASP 4.5 0.7 - - - -
122F ALA* 3.6 26.7 - - + +
125F HIS* 5.2 13.0 - - + +
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Residues in contact with PRO 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F PHE* 3.7 21.3 - - + -
84F VAL* 3.5 11.7 - - + +
85F LEU* 1.3 84.8 - - - +
87F VAL* 1.3 63.1 + - - +
97F PRO* 3.7 1.0 - - - +
98F TYR* 3.0 44.3 + - + +
99F PRO 3.4 26.7 - - - +
101F LEU* 4.7 4.5 - - + +
107F ARG* 5.6 0.7 - - - +
117F TRP* 4.1 4.5 - - + -
119F PHE* 3.5 33.0 - - + -
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Residues in contact with VAL 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LEU* 3.3 32.8 - - + +
86F PRO* 1.3 78.9 - - - +
88F TRP* 1.3 62.5 + - - +
89F LEU* 3.8 4.8 + - + +
95F PRO* 3.7 20.2 - - + -
96F GLN 3.5 24.7 - - - +
97F PRO* 4.5 3.1 - - + -
117F TRP* 3.3 7.5 - - - -
118F LEU* 2.7 64.1 + - + +
120F ARG* 4.8 4.3 - - + -
194F VAL* 4.9 6.3 - - + -
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Residues in contact with TRP 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F SER* 2.9 18.0 + - - -
87F VAL* 1.3 73.8 - - - +
89F LEU* 1.3 72.9 + - - +
90F ASN* 4.4 13.9 - - - -
91F PHE* 4.2 24.0 - + - -
95F PRO* 3.8 0.2 - - - +
96F GLN* 2.6 86.7 + - + +
98F TYR* 3.7 17.3 - + + -
115F HIS* 3.0 36.0 + + + -
116F LEU 3.5 12.6 - - - -
117F TRP* 3.5 42.6 - + + -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F LEU* 3.9 26.2 - - + +
64F ARG* 4.7 1.8 - - - -
65F SER* 2.5 29.5 + - - -
87F VAL* 4.6 4.3 - - + +
88F TRP* 1.3 76.0 + - - +
90F ASN* 1.3 65.9 + - - +
93F GLY 4.4 4.7 - - - +
94F GLU 3.7 0.9 - - - -
95F PRO* 3.9 24.2 - - + -
116F LEU* 2.8 42.7 + - + +
118F LEU* 4.4 13.7 - - + -
135F LEU* 4.9 9.2 - - + -
198F LEU* 4.0 37.0 - - + -
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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