Contacts of the strand formed by residues 116 - 121 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 4.3 11.2 - - + -
64I ARG 3.8 27.1 - - - +
65I SER* 3.0 12.4 + - - +
66I VAL* 6.1 0.9 - - + -
87I VAL 3.9 0.2 - - - +
88I TRP* 3.6 5.0 - - - -
89I LEU* 2.8 58.1 + - + +
114I GLY 3.6 13.5 - - - +
115I HIS* 1.3 79.8 - - - +
117I TRP* 1.3 63.8 + - - +
135I LEU* 4.2 23.8 - - + -
136I PHE 3.7 1.3 - - - -
137I VAL* 3.9 21.8 - - + -
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Residues in contact with TRP 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I PHE* 3.7 35.1 - + - -
86I PRO* 4.1 3.8 - - + -
87I VAL 3.3 12.3 - - - -
88I TRP* 3.5 49.4 - + + -
89I LEU* 5.7 0.2 - - - -
98I TYR* 3.5 45.1 - + + -
109I ILE* 4.4 13.5 - - + -
110I HIS 5.4 1.3 - - - -
111I SER* 3.2 26.1 + - - -
115I HIS* 4.5 0.6 - - - +
116I LEU* 1.3 79.4 - - - +
118I LEU* 1.3 64.9 + - - +
119I PHE* 4.0 16.9 - + + -
135I LEU* 3.4 7.4 - - - +
136I PHE* 2.8 44.3 + + + +
138I PRO* 3.9 23.3 - - + +
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Residues in contact with LEU 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I PRO 3.6 0.2 - - - -
87I VAL* 2.7 64.1 + - + +
89I LEU* 4.4 10.3 - - + -
117I TRP* 1.3 79.0 - - - +
119I PHE* 1.3 64.1 + - - +
120I ARG* 4.1 29.4 - - + +
134I GLU 4.3 5.8 - - - +
135I LEU* 3.6 23.1 - - + -
194I VAL* 3.7 30.1 - - + +
197I ASP* 6.0 1.8 - - + -
198I LEU* 4.1 18.2 - - + -
201I LEU* 5.7 2.0 - - + -
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Residues in contact with PHE 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I PHE* 3.6 34.8 - + - -
84I VAL* 4.0 13.2 - - + -
85I LEU 3.7 1.6 - - - -
86I PRO* 3.5 34.5 - - + -
117I TRP* 4.0 22.7 - + + -
118I LEU* 1.3 77.4 - - - +
120I ARG* 1.3 81.3 + - - +
128I LEU* 3.2 23.5 + - + +
129I LEU 5.3 0.7 - - - +
130I VAL* 3.5 43.7 - - + -
134I GLU 4.9 2.2 + - - -
136I PHE* 4.0 2.0 - + + -
149I ALA* 4.7 0.9 - - + -
151I ILE* 3.6 36.8 - - + -
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Residues in contact with ARG 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I VAL* 3.6 4.3 - - - -
85I LEU* 2.7 43.7 + - + +
87I VAL* 4.8 4.7 - - + -
118I LEU* 4.1 30.6 - - + +
119I PHE* 1.3 94.5 + - - +
121I ASP* 1.3 66.2 + - - +
125I HIS* 3.4 24.5 - - + +
126I ASP 3.3 8.7 - - - +
127I GLY* 3.5 13.7 - - - -
128I LEU* 3.5 20.1 + - - +
134I GLU* 3.9 26.3 + - - +
194I VAL* 3.9 29.5 - - + +
197I ASP* 2.6 37.8 + - - +
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Residues in contact with ASP 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ARG* 3.2 45.5 + - + +
83I VAL* 3.7 7.7 + - - +
85I LEU* 4.6 0.3 - - - +
120I ARG* 1.3 73.7 - - - +
122I ALA* 1.3 59.9 + - - +
123I GLY* 2.7 27.7 + - - -
124I THR* 2.9 31.3 + - - +
125I HIS* 2.8 28.8 + - - -
126I ASP* 3.0 16.9 + - + +
128I 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