Contacts of the strand formed by residues 121 - 129 (chain B) in PDB entry 2VQ5
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 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B TRP* 3.3 6.9 - - - -
114B LEU* 5.3 7.9 - - + +
115B VAL* 3.6 0.9 - - - -
116B ASP* 2.8 46.2 + - + +
119B HIS* 4.1 11.4 - - + +
120B ARG* 1.3 76.7 - - - +
122B LYS* 1.3 64.5 + - - +
123B LYS* 4.0 32.8 - - + -
142B THR* 4.0 16.2 - - + -
143B ILE 3.3 7.2 - - - +
144B HIS* 4.0 25.4 - - + +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 3.9 14.4 - - + -
63B TYR* 2.9 36.1 + - + +
64B SER* 5.4 0.2 - - - -
68B LEU* 3.8 12.9 - - - +
112B PHE* 3.4 43.3 - - + -
114B LEU 3.5 4.9 - - - -
115B VAL* 4.7 0.7 - - + +
121B LEU* 1.3 76.2 - - - +
123B LYS* 1.3 63.6 + - - +
124B VAL* 4.0 14.6 - - + -
141B ASP 3.8 0.3 - - - +
142B THR* 3.3 4.9 - - - +
143B ILE* 2.9 41.1 + - + +
1197B LDP 4.2 4.1 + - - -
1198B HBA 2.6 35.6 + - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.9 1.4 - - - -
113B ILE* 3.0 26.2 + - + -
114B LEU* 3.0 44.5 + - + +
121B LEU* 4.0 19.7 - - + -
122B LYS* 1.3 77.0 - - - +
124B VAL* 1.3 66.5 + - - +
125B GLN 4.3 0.4 - - - -
138B TYR* 5.8 2.4 + - - -
140B MSE 4.1 23.8 - - + +
141B ASP 3.3 4.3 - - - +
142B THR* 3.7 25.4 - - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 6.2 0.7 - - + -
110B GLU* 3.7 37.6 - - + +
111B LYS 3.3 12.1 - - - +
112B PHE* 4.5 8.7 - - + +
122B LYS* 4.0 24.5 - - + -
123B LYS* 1.3 79.6 - - - +
125B GLN* 1.3 61.6 + - - +
126B MSE 4.1 0.3 + - - -
139B TYR* 5.4 0.5 - - - -
140B MSE 3.8 2.8 - - - -
141B ASP* 2.9 38.9 + - - +
143B ILE* 5.0 1.1 - - + -
1197B LDP 4.8 5.8 - - - +
1198B HBA 3.6 31.4 - - + +
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Residues in contact with GLN 125 (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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110B GLU* 3.2 4.6 - - - -
111B LYS 2.8 35.9 + - - -
113B ILE* 2.8 35.6 - - + +
123B LYS 4.3 0.4 - - - -
124B VAL* 1.3 73.7 - - - +
126B MSE 1.3 70.3 + - - +
127B ILE* 3.5 15.4 + - + +
138B TYR* 4.0 19.1 - - - -
139B TYR 3.3 19.1 + - - +
140B MSE 3.6 23.3 - - + +
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Residues in contact with MSE 126 (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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108B TYR* 3.8 47.8 - - + -
109B LYS 3.5 11.9 - - - +
110B GLU* 4.2 8.6 + - - +
124B VAL 4.1 0.8 + - - -
125B GLN* 1.3 80.6 - - - +
127B ILE* 1.3 59.8 + - - +
128B GLU 4.3 1.6 - - - +
129B GLY 3.8 7.2 - - - +
131B TYR* 3.7 48.0 - - + -
132B LEU* 3.3 26.7 - - + +
139B TYR* 3.0 50.5 + - + +
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Residues in contact with ILE 127 (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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94B ILE* 4.0 28.7 - - + -
109B LYS* 2.8 38.1 + - + +
110B GLU 4.4 0.9 - - - +
111B LYS* 4.0 27.1 - - + -
113B ILE* 5.2 0.4 - - + -
125B GLN* 3.9 27.8 - - + +
126B MSE 1.3 75.1 - - - +
128B GLU* 1.3 64.8 + - + +
132B LEU* 3.4 11.5 - - - +
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Residues in contact with GLU 128 (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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101A PRO* 5.5 13.7 - - + +
106A HIS* 5.5 7.6 + - - -
108B TYR* 3.2 7.7 - - - +
109B LYS* 2.8 69.6 + - + +
126B MSE 4.3 0.5 - - - +
127B ILE* 1.3 84.4 - - + +
129B GLY* 1.3 65.4 + - - +
132B LEU* 3.5 5.6 - - - +
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Residues in contact with GLY 129 (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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106A HIS* 6.1 2.5 - - - -
107B GLU 3.8 7.2 - - - -
108B TYR* 3.9 1.1 - - - -
126B MSE 3.8 3.3 - - - +
128B GLU* 1.3 83.1 - - - +
130B GLY* 1.3 68.6 + - - -
131B TYR 3.3 0.5 + - - -
132B LEU* 3.2 24.7 + - - +
133B ASP* 3.8 20.8 + - - -
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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