Contacts of the strand formed by residues 252 - 260 (chain B) in PDB entry 2VES
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ALA 5.1 5.2 + - - -
87B GLY* 5.4 1.9 - - - -
89B ASP* 5.4 2.2 + - - -
126B LYS* 3.8 20.3 + - - -
127B LYS 4.1 2.8 + - - -
128B PHE* 3.4 30.3 - - - -
129B ILE* 2.9 25.5 + - - -
247B TYR* 4.0 20.4 + - - -
251B ASN* 1.3 75.4 - - - +
253B LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 253 (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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128B PHE* 5.1 1.0 - - - -
129B ILE* 3.5 17.7 - - + +
131B ILE* 3.9 20.4 - - + -
146B PHE* 3.4 30.7 - - + -
151B GLY 4.6 0.2 - - - -
152B PHE* 3.7 51.5 - - + +
246B LEU* 4.5 7.9 - - + +
249B LEU* 3.6 28.7 - - + -
251B ASN 3.7 1.7 + - - +
252B SER* 1.3 77.8 - - - +
254B ILE* 1.3 69.9 + - - +
255B GLY 3.8 11.9 - - - -
256B GLU 5.2 1.3 - - - -
257B PHE 5.3 0.2 - - - +
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Residues in contact with ILE 254 (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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128B PHE* 3.6 36.6 - - + -
129B ILE 2.8 9.6 + - - -
130B ARG* 3.8 25.4 - - + +
131B ILE* 2.9 29.5 + - - +
149B PHE 3.5 16.3 - - - +
150B ASP* 4.5 7.6 - - - +
151B GLY* 3.3 17.7 - - - +
253B LEU* 1.3 76.5 - - - +
255B GLY* 1.3 58.0 + - - +
284B VAL* 3.9 9.4 - - + -
286B PHE* 3.7 28.5 - - + -
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Residues in contact with GLY 255 (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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131B ILE* 4.1 9.6 - - - -
147B VAL 3.8 8.3 - - - -
149B PHE* 3.3 19.0 + - - -
151B GLY 2.7 10.9 + - - +
152B PHE* 3.4 7.4 - - - -
153B LYS 3.2 20.4 + - - -
253B LEU* 3.8 7.8 - - - -
254B ILE* 1.3 74.9 - - - +
256B GLU* 1.3 60.8 + - - -
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Residues in contact with GLU 256 (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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131B ILE* 4.9 0.6 - - - +
145B VAL 3.6 0.5 - - - +
146B PHE* 3.3 11.0 - - - -
147B VAL* 2.9 52.7 + - + +
148B PRO 5.1 0.2 - - - +
149B PHE* 3.7 20.7 - - + +
153B LYS* 3.2 37.2 + - + +
155B SER* 3.5 16.8 + - - -
253B LEU* 4.9 0.6 - - - +
255B GLY* 1.3 75.2 - - - -
257B PHE* 1.3 69.3 + - - +
258B ARG* 3.0 34.1 + - + +
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Residues in contact with PHE 257 (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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144B ALA* 4.0 9.2 - - + -
145B VAL 3.3 6.1 - - - -
146B PHE* 4.1 4.9 - + + -
152B PHE* 5.4 0.4 - - + -
153B LYS 2.9 9.5 + - - +
154B VAL* 3.5 21.2 - - + -
155B SER* 2.8 31.8 + - - -
156B PHE* 4.1 8.3 - + - -
242B ALA* 3.9 16.6 - - + -
246B LEU* 3.8 36.8 - - + -
253B LEU* 5.3 1.7 - - + +
255B GLY 4.4 0.2 + - - -
256B GLU* 1.3 75.4 - - - +
258B ARG* 1.3 59.2 + - - +
259B GLY* 3.4 30.1 - - - -
262B SER* 4.3 2.2 - - - -
267B ASN* 3.5 25.8 - - - -
270B LEU* 3.5 33.4 - - + -
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Residues in contact with ARG 258 (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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134B GLU* 5.2 0.8 + - - -
143B ARG 4.0 0.7 - - - +
144B ALA* 3.4 2.4 - - - -
145B VAL* 2.9 52.2 + - + +
147B VAL* 3.8 24.6 - - + +
155B SER* 3.3 14.4 - - - +
256B GLU* 3.0 38.7 + - + +
257B PHE* 1.3 80.1 - - - +
259B GLY* 1.3 59.3 + - - +
198C GLU* 4.0 42.1 + - - +
202C SER* 4.2 19.8 - - - -
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Residues in contact with GLY 259 (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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143B ARG 3.4 6.7 - - - -
155B SER 2.9 11.1 + - - +
156B PHE* 3.4 13.0 - - - -
157B GLU* 3.0 25.3 + - - +
257B PHE* 3.4 19.6 - - - -
258B ARG* 1.3 74.1 - - - +
260B PHE* 1.3 61.7 + - - +
261B LYS 4.1 0.7 - - - -
262B SER* 4.2 1.3 - - - -
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Residues in contact with PHE 260 (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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141B ASP* 3.3 31.6 - - + -
142B LYS* 3.3 2.8 - - - -
143B ARG* 2.8 47.1 + - + +
157B GLU* 3.4 29.8 - - + -
159B ASP* 3.9 12.8 - - + -
259B GLY* 1.3 73.0 - - - +
261B LYS* 1.3 92.4 + - + +
262B SER 3.1 0.3 + - - -
195C ARG* 3.4 56.3 - - + -
196C ASP* 5.9 3.1 - - - -
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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