Contacts of the strand formed by residues 256 - 263 (chain F) in PDB entry 3DUF
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 ALA 256 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204F ILE* 3.9 2.7 - - - +
205F THR* 3.3 15.3 - - + +
207F ILE* 4.6 6.3 - - + -
250F VAL* 3.9 29.6 - - + -
255F ARG* 1.3 76.9 - - - +
257F ILE* 1.3 71.0 + - - +
276F ILE* 5.0 0.7 - - + -
284F LEU* 4.8 3.8 - - - +
286F ALA 5.4 0.8 + - - -
287F PRO 4.2 2.4 - - - +
288F VAL* 3.3 39.5 - - + +
289F LEU 3.5 0.9 + - - -
321F VAL* 4.4 3.6 - - - +
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Residues in contact with ILE 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F ILE* 3.7 15.7 - - + -
205F THR 3.2 10.1 + - - +
206F ILE* 4.2 15.8 - - + +
207F ILE* 3.0 24.3 + - - +
256F ALA* 1.3 82.9 - - - +
258F VAL* 1.3 62.6 + - - +
259F VAL* 4.1 7.1 + - + -
288F VAL* 4.4 0.7 - - - -
289F LEU 3.2 11.9 - - - +
291F VAL* 4.6 1.8 - - + -
314F VAL* 4.0 35.2 - - + +
317F THR* 4.1 25.6 - - + +
318F ALA* 4.2 10.1 - - + +
321F VAL* 3.7 20.6 - - + -
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Residues in contact with VAL 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ILE* 3.6 32.5 - - + +
208F ALA* 5.9 0.2 - - - -
209F TYR* 6.0 1.6 - - + -
235F LEU* 6.3 0.4 - - + -
257F ILE* 1.3 75.7 - - - +
259F VAL* 1.3 63.2 + - - +
260F GLN* 5.7 0.2 - - + -
268F ILE* 5.6 2.5 - - + -
269F ALA* 3.7 34.4 - - + +
272F VAL* 4.6 12.6 - - + -
273F VAL* 3.8 24.2 - - + +
276F ILE* 5.1 0.4 - - + -
288F VAL* 4.0 11.0 - - + -
289F LEU 2.9 5.3 + - - -
290F ARG* 3.3 7.1 - - + +
291F VAL* 2.7 33.6 + - - +
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Residues in contact with VAL 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F ILE* 4.2 12.6 - - + -
207F ILE 2.8 21.2 + - - +
208F ALA* 3.8 19.1 - - + +
209F TYR* 3.9 8.5 + - - -
212F MET* 4.1 25.8 - - + +
216F SER* 4.1 13.0 - - - +
257F ILE* 4.5 4.5 - - + -
258F VAL* 1.3 81.9 - - - +
260F GLN* 1.3 68.1 + - - +
291F VAL* 3.5 32.5 - - + -
314F VAL* 3.9 22.0 - - + -
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Residues in contact with GLN 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F TYR* 3.5 22.8 + - + +
212F MET* 3.9 9.8 - - - +
259F VAL* 1.3 78.1 - - - +
261F GLU* 1.3 60.7 + - - +
262F ALA* 3.3 12.8 + - - +
263F GLN 2.8 29.9 + - - -
264F ARG* 4.4 2.8 + - - +
266F ALA 2.9 11.7 + - - -
267F GLY* 3.5 4.0 - - - -
268F ILE 3.2 9.4 + - - -
269F ALA* 2.9 44.9 + - + +
291F VAL 3.0 15.3 + - - +
292F ALA* 3.5 24.2 - - + +
309F PRO* 3.9 8.0 - - - +
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Residues in contact with GLU 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F PHE* 5.8 0.9 - - + -
119F GLY* 3.5 6.6 - - - -
120F GLY 3.0 26.2 + - - +
131F SER* 3.7 14.9 + - - +
172F HIS* 2.9 28.2 + - - -
209F TYR* 4.9 3.8 + - - -
211F ALA* 4.3 1.9 + - - +
212F MET* 3.7 28.9 - - + +
260F GLN* 1.3 70.7 - - - +
262F ALA* 1.3 69.7 + - - +
293F ALA* 3.4 17.3 - - - +
298F TYR* 4.5 5.9 - - + -
307F TRP* 4.4 4.8 - - + -
308F LEU* 3.5 29.2 - - + +
309F PRO* 4.1 9.1 - - + +
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Residues in contact with ALA 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F SER* 3.9 24.0 - - - +
133F GLU* 3.5 23.5 + - - +
260F GLN* 3.3 21.7 + - - +
261F GLU* 1.3 84.3 - - - +
263F GLN* 1.3 68.7 + - - +
266F ALA* 4.2 2.0 - - + -
267F GLY* 3.9 13.5 - - - +
292F ALA* 3.4 2.3 - - - +
293F ALA* 3.1 12.8 + - - -
307F TRP* 5.5 0.7 - - - -
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Residues in contact with GLN 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ASP* 5.7 2.0 + - - +
131F SER 4.5 8.2 + - - +
132F LEU* 6.1 0.2 - - - +
260F GLN* 2.8 17.5 + - - -
262F ALA* 1.3 77.0 - - - +
264F ARG* 1.3 65.8 + - - +
265F GLN* 3.3 6.1 - - + +
266F ALA* 3.0 25.4 + - + +
293F ALA* 3.5 8.3 - - - +
294F PRO 3.1 23.3 - - - +
295F ASP* 3.8 9.9 - - - +
296F THR 2.9 24.4 + - - +
297F VAL* 4.0 1.6 - - - +
298F TYR* 3.7 20.4 - - - +
307F TRP* 4.2 13.7 - - + -
138H GLN 5.2 0.2 - - - +
140H PRO* 4.3 12.7 - - + +
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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