Contacts of the strand formed by residues 42 - 52 (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 VAL 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B THR* 1.3 75.9 - - - +
43B THR* 1.3 74.8 + - - +
44B LYS* 4.4 11.4 - - + -
162B HIS* 3.1 5.2 - - - -
163B VAL* 2.7 38.3 + - + +
165B PRO* 4.3 20.2 - - + -
168B VAL* 4.2 20.0 - - + -
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Residues in contact with THR 43 (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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41B THR* 4.1 3.2 + - - -
42B VAL* 1.3 78.4 - - - +
44B LYS* 1.3 67.5 + - - +
45B VAL* 4.3 11.0 - - + -
160B GLU* 4.1 16.2 - - + +
161B TYR 3.6 3.1 - - - -
162B HIS* 3.2 33.4 + - + -
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Residues in contact with LYS 44 (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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42B VAL* 4.0 13.2 + - + -
43B THR* 1.3 78.9 - - - +
45B VAL* 1.3 71.3 + - - +
46B ILE* 3.9 21.3 - - - +
159B THR 3.8 1.3 - - - +
160B GLU* 3.3 3.6 - - - +
161B TYR* 2.8 76.0 + - + +
163B VAL* 4.7 4.3 - - + -
168B VAL* 6.2 2.9 - - + -
172B GLU* 5.4 16.2 + - + +
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Residues in contact with VAL 45 (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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43B THR* 4.3 10.1 - - + -
44B LYS* 1.3 85.0 + - - +
46B ILE* 1.3 69.5 + - - +
47B HIS* 3.4 36.1 - - + +
158B SER* 4.7 4.7 - - - +
159B THR 3.5 10.3 - - - +
160B GLU* 3.9 25.4 - - + +
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Residues in contact with ILE 46 (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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44B LYS* 3.9 22.9 - - - +
45B VAL* 1.3 79.1 - - - +
47B HIS* 1.3 63.3 - - - +
158B SER* 3.2 7.1 - - - -
159B THR* 3.0 46.7 + - + +
161B TYR* 5.0 7.0 - - + +
175B ILE* 3.9 22.4 - - + +
176B THR* 3.5 40.2 - - - +
177B THR* 3.7 13.8 - - + +
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Residues in contact with HIS 47 (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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45B VAL* 3.4 32.8 - - + +
46B ILE* 1.3 81.3 - - - +
48B HIS* 1.3 64.6 + - - +
49B GLU* 5.7 4.7 - - + -
156B LYS* 6.1 2.6 - - - -
157B SER 3.5 5.1 + - - +
158B SER* 3.6 16.9 - - - -
177B THR* 3.6 10.7 + - - +
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Residues in contact with HIS 48 (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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47B HIS* 1.3 76.7 - - - +
49B GLU* 1.3 85.1 + - - +
50B LEU* 4.0 20.0 - - + +
155B ILE 3.7 2.1 - - - +
156B LYS* 3.7 0.3 - - - -
157B SER* 2.9 44.2 + - - +
177B THR* 3.8 22.1 + - + +
180B LEU* 5.6 0.2 - - + -
181B ALA* 3.7 40.4 + - + +
184B ALA* 4.5 6.8 - - + +
185B ASP* 5.0 3.3 + - - -
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Residues in contact with GLU 49 (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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47B HIS* 5.7 4.9 - - + -
48B HIS* 1.3 93.2 + - - +
50B LEU* 1.3 64.2 + - - +
154B VAL* 4.0 14.5 - - + +
155B ILE 3.3 5.8 - - - -
156B LYS* 3.2 38.5 + - + -
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Residues in contact with LEU 50 (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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48B HIS* 4.0 13.2 - - + +
49B GLU* 1.3 78.4 - - - +
51B GLU* 1.3 72.7 + - - +
52B VAL* 3.6 32.2 - - + +
154B VAL* 3.5 3.9 - - - +
155B ILE* 2.8 39.6 + - + +
184B ALA* 4.3 18.2 - - + +
185B ASP* 3.9 20.9 - - - +
188B SER* 3.6 20.6 - - - +
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Residues in contact with GLU 51 (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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49B GLU 4.3 0.2 - - - -
50B LEU* 1.3 85.8 - - - +
52B VAL* 1.3 63.5 + - - +
148B THR* 5.9 0.7 - - + -
153B CYS 3.6 5.4 - - - +
154B VAL* 3.8 23.6 - - + +
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Residues in contact with VAL 52 (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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50B LEU* 3.6 28.5 - - + +
51B GLU* 1.3 81.7 - - - +
53B ALA* 1.3 61.1 + - - +
54B ALA* 2.9 20.3 + - + +
59B ILE* 3.7 23.1 - - + -
152B SER* 3.3 4.9 - - - -
153B CYS* 2.9 40.2 + - - +
155B ILE* 3.8 17.3 - - + -
188B SER* 3.8 18.2 - - - -
192B LEU* 4.3 12.8 - - + -
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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