Contacts of the strand formed by residues 152 - 163 (chain A) 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 SER 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU* 4.4 5.9 + - - -
52A VAL 3.4 11.4 - - - -
53A ALA* 4.4 4.7 - - - -
54A ALA 3.1 8.9 + - - -
55A SER* 4.2 0.6 - - - +
56A ALA 4.4 2.8 + - - -
147A PRO* 3.8 1.7 - - - +
148A THR* 2.8 46.9 + - - -
149A GLY* 3.1 12.7 + - - +
150A LYS 3.7 0.2 - - - -
151A ASP* 1.3 81.8 + - - +
153A CYS* 1.3 61.3 + - - +
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Residues in contact with CYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.3 5.0 - - - +
52A VAL* 2.9 40.0 + - - +
54A ALA 3.2 13.8 + - - -
56A ALA* 3.6 20.2 - - + +
59A ILE* 3.7 27.1 - - - -
145A VAL* 3.7 16.4 - - + -
146A VAL 3.2 16.6 - - - +
148A THR* 3.4 8.9 + - - -
152A SER* 1.3 76.9 - - - +
154A VAL* 1.3 58.9 + - - +
155A ILE* 4.6 3.1 - - - -
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 4.0 24.2 - - + +
50A LEU 3.5 4.7 - - - +
51A GLU* 3.7 29.8 - - + +
144A HIS 3.4 4.2 - - - +
145A VAL* 3.5 1.7 - - - +
146A VAL* 2.8 63.1 + - + +
148A THR* 3.7 14.6 - - + +
153A CYS* 1.3 72.6 - - - +
155A ILE* 1.3 61.2 + - - +
156A LYS* 3.5 20.8 + - + -
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 3.6 1.4 - - - +
49A GLU* 3.3 4.7 - - - -
50A LEU* 2.8 40.9 + - + +
52A VAL* 4.3 8.3 - - + -
59A ILE* 3.7 30.3 - - + -
63A TYR* 3.6 25.1 - - + +
143A ILE* 3.8 14.4 - - + -
144A HIS 3.9 2.7 - - - -
145A VAL* 4.5 6.7 - - + +
153A CYS* 4.6 4.5 - - - -
154A VAL* 1.3 71.9 - - - +
156A LYS* 1.3 58.1 + - - +
157A SER* 3.5 16.9 + - - +
184A ALA* 4.0 18.4 - - + +
188A SER* 3.5 25.6 - - - +
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS 3.5 7.4 - - - +
49A GLU* 4.3 26.0 + - + +
142A THR 3.5 1.9 - - - +
143A ILE* 3.4 2.3 - - - -
144A HIS* 2.8 48.2 + - + +
146A VAL* 3.8 25.0 - - + +
154A VAL* 3.8 24.9 - - + +
155A ILE* 1.3 74.2 - - - +
157A SER* 1.3 59.7 + - - +
158A SER* 4.1 1.1 + - - -
1202A CL 3.8 27.0 - - + +
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 2.7 54.5 + - - +
63A TYR* 4.6 1.0 + - - -
142A THR 3.3 5.8 - - - -
143A ILE* 4.0 9.9 - - - +
155A ILE* 3.5 21.2 + - - +
156A LYS* 1.3 71.3 - - - +
158A SER* 1.3 57.9 + - - +
177A THR* 4.0 1.6 - - - +
180A LEU* 3.8 39.5 + - - +
184A ALA* 4.6 0.5 - - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 4.4 6.3 - - - +
46A ILE 3.3 13.2 - - - -
47A HIS* 3.8 25.2 + - - -
140A MSE 3.7 0.7 - - - +
141A ASP* 3.3 4.2 - - - -
142A THR* 2.8 54.5 + - - +
156A LYS 4.1 1.7 + - - -
157A SER* 1.3 76.3 - - - +
159A THR* 1.3 63.6 + - - +
160A GLU 4.1 0.6 + - - -
180A LEU* 3.7 3.4 - - - +
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS 3.7 1.2 - - - +
45A VAL* 3.4 5.2 - - - -
46A ILE* 2.9 45.8 + - - +
139A TYR* 3.4 44.1 + - + +
140A MSE 3.4 4.3 - - - +
141A ASP* 2.6 17.2 + - - +
158A SER* 1.3 73.9 - - - +
160A GLU* 1.3 61.1 + - - +
161A TYR* 4.1 13.7 - - + -
175A ILE* 4.5 3.6 - - + -
176A THR 5.0 2.4 + - - -
177A THR* 4.7 3.1 - - - +
180A LEU* 3.4 13.5 - - - +
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR* 3.5 22.6 - - + +
44A LYS 3.4 4.7 - - - +
45A VAL* 4.0 14.7 - - + +
138A TYR* 3.9 16.9 + - + -
139A TYR* 3.5 1.2 - - - -
140A MSE 2.9 42.5 + - + +
158A SER* 4.1 0.8 + - - -
159A THR* 1.3 73.7 - - - +
161A TYR* 1.3 61.6 + - - +
162A HIS* 2.8 29.5 + - + -
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL 3.8 0.7 - - - +
43A THR* 4.2 0.2 - - - +
44A LYS* 2.9 66.2 + - + +
46A ILE* 4.6 15.5 - - + +
136A VAL* 4.0 8.5 - - + -
138A TYR 3.1 13.2 - - - +
139A TYR* 3.9 15.0 - - + -
159A THR* 4.1 10.8 - - + -
160A GLU* 1.3 74.4 - - - +
162A HIS* 1.3 66.5 + - - +
163A VAL* 3.4 29.4 - - + -
171A VAL* 4.3 6.5 - - + +
172A GLU* 4.1 28.4 - - - +
175A ILE* 3.6 48.1 + - + +
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Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 3.4 20.9 - - - +
42A VAL 3.3 4.9 - - - +
43A THR* 3.0 23.9 + - + -
136A VAL* 3.3 5.6 - - - +
137A THR* 2.8 42.0 + - - +
138A TYR* 2.9 40.8 + + + -
160A GLU* 2.8 34.9 + - - -
161A TYR* 1.3 76.4 + - - +
163A VAL* 1.3 58.0 + - - +
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 3.6 5.4 - - - -
42A VAL* 2.7 44.7 + - + +
44A LYS* 4.4 5.2 - - + -
134A LEU 4.6 0.2 - - - +
135A GLY 3.4 17.7 - - - +
136A VAL* 3.5 22.4 - - + -
161A TYR* 3.4 27.6 - - + -
162A HIS* 1.3 72.3 - - - +
164A LYS* 1.3 69.7 + - - +
165A PRO 3.3 0.5 - - - -
167A PHE* 4.3 6.7 - - + -
168A VAL* 4.3 15.0 - - + -
171A VAL* 3.7 17.7 - - + -
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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