Contacts of the strand formed by residues 116 - 121 (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 LEU 116 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63F LEU* 4.2 17.0 - - + -
64F ARG 3.9 21.8 - - - +
65F SER* 3.0 9.9 + - - +
66F VAL* 6.1 0.4 - - + -
88F TRP* 3.5 4.9 - - - -
89F LEU* 2.8 58.1 + - + +
114F GLY 3.6 11.4 - - - +
115F HIS* 1.3 81.4 - - - +
117F TRP* 1.3 64.0 + - - +
135F LEU* 4.2 23.8 - - + -
136F PHE 3.7 1.3 - - - +
137F VAL* 3.9 21.1 - - + -
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Residues in contact with TRP 117 (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* 3.8 34.4 - + - -
86F PRO* 4.1 3.4 - - + -
87F VAL 3.3 12.6 - - - -
88F TRP* 3.5 50.6 - + + -
89F LEU* 5.6 0.2 - - - -
98F TYR* 3.5 45.1 - + + -
109F ILE* 4.4 13.5 - - + -
110F HIS 5.4 1.6 - - - -
111F SER* 3.2 26.1 + - - -
115F HIS 4.6 0.2 - - - -
116F LEU* 1.3 79.9 - - - +
118F LEU* 1.3 66.1 + - - +
119F PHE* 4.0 17.3 - + + -
135F LEU* 3.5 8.1 - - - +
136F PHE* 2.9 40.8 + + + +
138F PRO* 3.9 23.5 - - + +
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Residues in contact with LEU 118 (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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87F VAL* 2.7 64.6 + - + +
89F LEU* 4.4 11.2 - - + -
117F TRP* 1.3 79.4 - - - +
119F PHE* 1.3 66.0 + - - +
120F ARG* 4.0 31.9 - - + +
134F GLU 4.3 4.9 - - - +
135F LEU* 3.7 22.2 - - + -
194F VAL* 4.1 23.8 - - + +
197F ASP* 5.9 2.2 - - + -
198F LEU* 4.2 18.4 - - + -
201F LEU* 5.4 2.7 - - + -
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Residues in contact with PHE 119 (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* 3.6 33.7 - + - -
84F VAL* 4.0 13.9 - - + -
85F LEU 3.7 2.2 - - - -
86F PRO* 3.5 34.3 - - + -
117F TRP* 4.0 22.9 - + + -
118F LEU* 1.3 76.3 - - - +
120F ARG* 1.3 80.5 + - - +
128F LEU* 3.2 23.2 + - + +
129F LEU 5.6 0.2 - - - -
130F VAL* 3.5 43.3 - - + -
134F GLU 4.8 2.2 + - - -
136F PHE* 4.0 3.1 - + + -
149F ALA* 4.7 0.9 - - + -
151F ILE* 3.7 37.5 - - + -
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Residues in contact with ARG 120 (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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84F VAL* 3.6 4.7 - - - -
85F LEU* 2.8 41.8 + - + +
87F VAL* 4.8 4.7 - - + -
118F LEU* 4.0 30.6 - - + +
119F PHE* 1.3 94.9 + - - +
121F ASP* 1.3 67.1 + - - +
125F HIS* 3.4 24.9 - - + +
126F ASP 3.3 10.1 - - - +
127F GLY* 3.5 12.7 - - - -
128F LEU* 3.5 16.0 + - - +
134F GLU* 3.9 30.9 + - - +
194F VAL* 4.0 27.5 - - + +
197F ASP* 2.5 39.2 + - - +
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Residues in contact with ASP 121 (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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82F ARG* 3.3 45.2 + - + +
83F VAL* 3.6 8.2 + - - +
85F LEU* 4.6 0.3 - - - +
120F ARG* 1.3 74.4 - - - +
122F ALA* 1.3 58.6 + - - +
123F GLY* 2.8 26.9 + - - -
124F THR* 2.8 32.3 + - - +
125F HIS* 2.8 28.2 + - - -
126F ASP* 3.0 16.3 + - + +
128F LEU* 3.6 8.3 - - + +
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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