Contacts of the strand formed by residues 284 - 292 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121J TYR* 4.3 12.4 + - + -
276J THR* 4.2 9.4 - - + -
277J LEU 3.0 18.8 - - - +
278J GLU* 6.0 0.7 - - + -
283J GLN* 1.3 86.4 - - + +
285J LEU* 1.3 67.1 + - - +
286J GLY 3.3 4.3 - - - +
287J ARG* 3.2 70.9 - - + +
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Residues in contact with LEU 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J TYR* 3.2 22.4 - - - -
122J PRO 3.7 4.5 - - - +
124J PRO* 3.4 18.4 - - + +
125J HIS* 3.9 30.6 + - + +
127J PHE* 4.0 5.7 - - + -
169J PRO* 4.5 2.5 - - + -
170J PRO* 3.9 12.8 - - + -
173J THR* 5.0 0.4 - - - +
277J LEU* 3.6 29.9 + - + +
279J MET* 3.8 33.4 - - + -
283J GLN 3.6 13.5 - - - +
284J VAL* 1.3 81.4 - - - +
286J GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J TYR* 3.5 20.3 - - - -
127J PHE* 3.0 43.8 - - - -
275J ILE 4.6 1.2 - - - +
277J LEU 4.0 3.3 + - - -
284J VAL* 3.3 6.5 - - - +
285J LEU* 1.3 83.3 - - - +
287J ARG* 1.3 64.5 + - - +
288J ARG 4.0 0.3 + - - -
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Residues in contact with ARG 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J SER* 3.1 37.0 + - - -
118J ASN* 4.7 2.2 - - - +
119J THR* 2.9 45.1 + - - +
120J ASP 3.8 0.2 - - - -
121J TYR* 3.1 44.1 + - + +
274J ILE* 5.4 2.5 - - + -
275J ILE 3.7 5.8 - - - -
276J THR* 3.7 22.3 - - + +
284J VAL* 3.2 33.5 - - + +
286J GLY* 1.3 73.2 - - - -
288J ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J THR 5.7 0.4 - - - -
120J ASP* 3.3 29.7 + - - +
121J TYR 3.7 19.2 + - - +
122J PRO* 4.0 13.9 - - - +
127J PHE* 2.8 44.0 + - + -
128J GLU* 3.6 21.0 + - - -
129J VAL* 3.1 54.0 + - + +
274J ILE* 3.4 5.8 - - - +
275J ILE* 3.2 36.3 + - + +
286J GLY 4.0 0.6 + - - +
287J ARG* 1.3 83.3 - - - +
289J SER* 1.3 65.8 + - - +
290J PHE* 5.5 1.3 - - + -
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Residues in contact with SER 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J ASN* 3.6 27.8 + - - +
119J THR 4.4 0.3 + - - -
120J ASP* 3.3 26.7 + - - +
129J VAL* 5.4 0.4 - - - +
149J LYS* 5.7 2.4 + - - -
272J LEU* 4.8 8.3 - - - +
273J ILE 3.1 12.8 - - - -
274J ILE* 4.0 17.3 - - - -
288J ARG* 1.3 80.8 - - - +
290J PHE* 1.3 65.6 + - - +
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Residues in contact with PHE 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J VAL* 4.9 10.5 - - + -
131J PHE* 3.0 43.5 - + - -
144J TYR* 4.2 8.5 - + - +
149J LYS* 3.8 15.9 - - + +
151J LEU* 3.1 42.0 - - + -
161J ILE* 4.8 6.1 - - + -
256J PHE* 5.8 1.8 - + - -
272J LEU* 3.1 7.8 - - - +
273J ILE* 2.7 62.1 + - + -
275J ILE* 4.4 13.9 - - + -
288J ARG* 5.5 0.9 - - + -
289J SER* 1.3 79.0 - - - +
291J GLU* 1.3 62.0 + - - +
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Residues in contact with GLU 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J LEU* 5.3 5.2 - - - +
149J LYS 3.7 8.2 + - - +
150J LYS* 3.0 43.1 + - + +
151J LEU* 2.8 33.4 + - - +
182J LYS* 3.1 45.5 + - + +
270J PRO* 4.1 13.0 - - - +
271J ILE 3.2 17.5 - - - +
272J LEU* 3.9 2.5 - - + +
273J ILE* 4.8 0.2 - - - -
290J PHE* 1.3 76.3 - - - +
292J GLY* 1.3 64.7 + - - +
293J ARG* 5.0 5.0 - - - +
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Residues in contact with GLY 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J LEU* 3.4 18.4 - - - -
260J SER* 3.7 3.3 + - - -
270J PRO* 5.7 0.2 - - - +
271J ILE* 3.1 40.3 + - - +
272J LEU* 4.2 1.0 - - - +
273J ILE* 4.5 10.0 - - - +
290J PHE 4.0 1.0 + - - -
291J GLU* 1.3 76.9 - - - +
293J ARG* 1.3 60.0 + - - -
294J ILE* 3.6 6.1 + - - +
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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