Contacts of the strand formed by residues 119 - 124 (chain B) in PDB entry 3VRY
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 TRP 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TYR* 3.1 28.9 - + - -
98B HIS* 4.0 23.6 - + - -
101B ASP* 4.0 5.6 - - + -
116B SER* 3.3 27.7 + - - +
118B GLU* 1.3 84.2 - - + +
120B TRP* 1.3 63.7 + - - +
132B TYR* 3.9 31.3 - + + -
133B ILE 3.3 27.4 - - - -
134B PRO* 3.7 17.3 - - + -
253B LYS* 4.3 2.5 - - - -
254B PRO* 3.5 36.8 - - + +
255B TRP 3.0 22.3 + - - -
257B LYS* 3.7 39.7 - - + +
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Residues in contact with TRP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 6.2 0.2 - - + -
88B VAL* 4.3 12.3 - - + -
112B VAL* 4.0 29.8 - - + -
114B GLU 3.2 8.5 - - - +
115B GLU* 3.4 40.9 - - + +
116B SER 3.4 17.0 - - - -
117B GLY* 3.1 26.3 + - - +
118B GLU 4.0 0.2 + - - -
119B TRP* 1.3 73.5 - - - +
121B LYS* 1.3 65.1 + - - +
122B ALA* 5.5 0.2 - - + -
132B TYR* 3.2 7.7 - - - -
133B ILE* 2.8 46.7 + - + +
135B SER* 3.7 20.0 - - - -
138B VAL* 4.6 15.9 - - + -
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 3.7 2.9 - - - +
113B LEU* 2.6 48.0 + - + +
114B GLU* 2.9 37.5 + - + +
116B SER* 5.1 1.4 + - - +
120B TRP* 1.3 70.0 - - - +
122B ALA* 1.3 60.0 + - - +
130B GLU* 4.5 16.3 + - - +
131B GLY* 3.4 22.4 - - - +
132B TYR* 4.0 31.8 - - + +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.5 4.3 - - - +
110B MET* 3.6 25.1 - - + -
111B VAL 3.2 13.7 - - - +
112B VAL* 4.6 3.1 - - + -
113B LEU* 3.9 7.4 - - - +
120B TRP* 5.5 0.4 - - + -
121B LYS* 1.3 77.4 - - - +
123B ARG* 1.3 59.9 + - - +
130B GLU* 3.3 2.3 - - - -
131B GLY 2.7 40.2 + - - +
133B ILE* 3.7 23.8 - - + -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ARG* 4.5 4.9 - - - +
110B MET* 3.2 4.4 - - - -
111B VAL* 2.6 57.6 + - + +
113B LEU* 3.4 26.1 - - + +
122B ALA* 1.3 73.7 - - - +
124B SER* 1.3 69.2 + - - +
125B LEU 3.6 0.7 + - - -
128B ARG* 3.8 34.7 - - - +
129B LYS 3.5 5.4 - - - +
130B GLU* 3.0 37.1 + - + -
603B CL 3.3 22.9 - - - +
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.3 4.9 - - - -
103B SER 5.5 4.1 + - - -
104B PHE* 5.8 2.8 - - - +
108B ASP* 4.9 3.3 + - - +
109B GLN 4.6 0.3 + - - -
110B MET* 3.8 27.8 - - - +
123B ARG* 1.3 72.9 - - - +
125B LEU* 1.3 55.5 + - - +
126B ALA* 3.1 11.1 + - - +
127B THR* 3.0 31.8 + - - +
128B ARG* 2.7 35.3 + - - -
129B LYS 3.0 11.9 + - - -
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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