Contacts of the strand formed by residues 284 - 294 (chain B) in PDB entry 3VD1
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 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B TYR* 3.1 20.1 + - + -
276B THR* 4.6 2.7 - - + -
277B LEU 3.9 5.6 - - - +
278B GLU* 4.3 17.7 - - + +
283B GLN* 1.3 68.6 - - - +
285B LEU* 1.3 57.4 + - - +
286B GLY* 2.9 31.2 - - - +
287B ARG* 3.5 39.9 - - - +
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Residues in contact with LEU 285 (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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121B TYR* 3.5 5.2 - - - -
122B PRO 3.5 1.6 - - - +
123B GLY* 3.0 25.5 - - - -
124B PRO* 3.0 19.3 - - + +
125B HIS* 3.4 31.9 - - + +
170B PRO* 4.0 15.5 - - + -
173B THR* 4.5 5.6 - - + +
277B LEU* 3.2 21.8 + - + +
278B GLU* 3.4 21.5 - - - +
279B MET* 3.3 35.9 - - + -
283B GLN 3.0 16.0 + - - +
284B VAL* 1.3 73.0 - - - +
286B GLY* 1.3 55.8 + - - +
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Residues in contact with GLY 286 (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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121B TYR* 2.9 20.2 - - - -
122B PRO 3.5 6.3 - - - -
276B THR* 3.8 0.7 - - - -
277B LEU* 3.3 27.4 + - - +
284B VAL* 2.9 16.3 - - - +
285B LEU* 1.3 82.0 - - - +
287B ARG* 1.3 68.0 + - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 6.2 1.0 - - - +
117B SER* 3.1 39.0 + - - +
119B THR* 3.0 29.1 + - - +
121B TYR* 2.8 36.4 + - + +
122B PRO 4.4 0.2 - - - -
127B PHE* 3.7 8.0 - - - -
274B ILE* 3.5 24.0 - - + -
275B ILE 3.4 10.3 - - - +
276B THR* 3.4 28.4 - - + +
277B LEU* 3.8 2.4 - - - +
284B VAL* 3.5 32.6 - - - +
286B GLY* 1.3 76.9 - - - +
288B ARG* 1.3 85.1 + - - +
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ASP* 3.2 40.1 + - - +
121B TYR 4.9 1.6 - - - +
122B PRO* 5.4 11.9 - - + +
127B PHE* 3.6 28.6 + - + +
128B GLU* 5.9 0.2 - - - -
129B VAL* 3.6 17.7 - - + +
273B ILE 3.7 0.5 - - - +
274B ILE* 3.3 14.2 - - - +
275B ILE* 3.5 19.0 + - + +
287B ARG* 1.3 84.1 + - - +
289B SER* 1.3 74.0 + - - +
290B PHE* 5.6 2.5 - - + -
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 3.3 16.9 + - - -
120B ASP* 3.6 10.9 + - - +
144B TYR* 5.3 0.2 + - - -
149B LYS* 3.5 29.9 - - - +
272B LEU* 4.0 14.0 - - - +
273B ILE 3.6 6.7 - - - -
274B ILE* 3.3 15.9 - - - +
287B ARG* 4.9 0.3 - - - +
288B ARG* 1.3 92.9 + - - +
290B PHE* 1.3 71.5 + - - +
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Residues in contact with PHE 290 (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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129B VAL* 4.5 6.1 - - + -
131B PHE* 3.6 31.4 - + - -
144B TYR* 3.9 9.2 - - + +
149B LYS* 3.2 26.5 - - + +
151B LEU* 3.5 29.2 - - + -
161B ILE* 4.2 5.8 - - + -
256B PHE* 5.6 1.6 - + - -
272B LEU* 4.1 4.3 - - - -
273B ILE* 3.1 53.5 + - + -
275B ILE* 3.5 31.4 - - + -
288B ARG* 5.6 0.9 - - + -
289B SER* 1.3 83.7 - - - +
291B GLU* 1.3 68.0 + - - +
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Residues in contact with GLU 291 (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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148B LEU* 5.6 1.6 - - - +
149B LYS* 2.6 29.9 + - + +
150B LYS* 2.6 48.2 + - + +
151B LEU 2.8 15.6 + - - -
182B LYS* 4.1 14.3 - - + +
270B PRO* 3.1 27.2 - - + +
271B ILE 3.4 16.8 - - - +
272B LEU* 3.7 15.3 - - + +
290B PHE* 1.3 74.6 - - - +
292B GLY* 1.3 66.5 + - - +
293B ARG* 4.9 0.9 - - - +
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Residues in contact with GLY 292 (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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150B LYS* 5.2 0.2 - - - -
151B LEU* 3.2 16.4 - - - -
153B CYS* 6.3 0.2 - - - -
260B SER* 3.8 3.5 + - - -
270B PRO* 5.2 0.9 - - - +
271B ILE* 3.1 33.7 + - - +
272B LEU* 4.8 0.2 - - - +
273B ILE* 4.7 14.0 - - - +
290B PHE 3.7 2.4 + - - -
291B GLU* 1.3 83.8 - - - +
293B ARG* 1.3 61.7 + - - +
294B ILE* 5.2 1.6 - - - -
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Residues in contact with ARG 293 (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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150B LYS* 3.7 25.0 - - + +
151B LEU 2.8 11.5 + - - +
152B TYR* 3.5 15.6 - - + -
153B CYS* 2.5 36.2 + - - +
260B SER* 3.2 22.3 - - - +
261B SER* 5.5 3.2 - - - -
268B ARG 5.8 1.4 + - - -
270B PRO* 6.1 3.8 - - + -
291B GLU* 4.9 1.6 - - - +
292B GLY* 1.3 74.0 - - - +
294B ILE* 1.3 59.0 + - - +
295B CYS* 3.9 11.0 + - - +
301B ASP* 2.4 41.4 + - - +
305B ASP* 4.8 12.3 + - - +
404E T 2.9 51.6 + - - -
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Residues in contact with ILE 294 (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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153B CYS* 2.9 15.5 - - + +
154B GLN 3.9 2.2 - - - +
155B ILE* 3.7 25.4 - - - +
214B LEU* 4.1 10.1 - - + -
256B PHE* 3.4 34.1 - - + +
258B CYS 2.8 33.0 - - - +
259B ASN* 3.1 13.5 - - - +
260B SER* 2.6 40.0 + - - +
266B MET* 4.0 15.9 - - + -
271B ILE* 4.7 6.5 - - + -
292B GLY 5.2 2.2 - - - -
293B ARG* 1.3 78.5 - - - +
295B CYS* 1.3 58.8 + - - +
405E G 4.1 1.9 + - - -
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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