Contacts of the strand formed by residues 282 - 291 (chain A) in PDB entry 5TWV
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 GLU 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA 3.8 17.8 - - - +
34A ARG* 3.9 3.3 - - - +
35A PHE* 3.8 29.6 + - + +
36A VAL 3.9 5.5 - - - +
219A VAL* 4.0 1.9 - - - +
220A VAL* 3.0 46.3 + - + +
281A LEU* 1.3 82.1 - - - +
283A ILE* 1.3 66.3 + - - +
303A SER* 2.8 32.2 + - - +
304A TYR 3.9 6.7 - - - +
305A LEU* 3.9 31.5 - - + +
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Residues in contact with ILE 283 (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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198A PHE* 5.1 21.1 - - + -
200A LEU* 5.9 3.4 - - + -
217A MET* 5.2 4.0 - - + -
218A GLN 3.5 16.8 - - - +
219A VAL* 4.1 25.8 - - + -
238A ILE* 5.1 12.3 - - + -
267A LEU* 4.7 23.6 - - + -
281A LEU* 4.5 9.4 - - + -
282A GLU* 1.3 78.9 - - - +
284A ILE* 1.3 67.3 + - - +
285A VAL* 4.1 2.1 + - + +
303A SER* 3.5 4.3 + - - -
304A TYR* 3.1 39.6 + - + +
309A ILE* 4.6 18.6 - - + -
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Residues in contact with ILE 284 (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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35A PHE* 3.9 20.4 - - + -
36A VAL* 3.9 19.3 - - + -
217A MET* 3.5 7.8 - - - +
218A GLN* 2.9 56.9 + - + +
220A VAL* 5.0 13.0 - - + -
235A GLN* 4.4 10.5 - - - +
282A GLU 4.2 0.4 - - - -
283A ILE* 1.3 74.8 - - - +
285A VAL* 1.3 61.9 + - - +
286A ILE* 3.9 16.1 - - + +
301A ARG* 6.3 1.6 - - + -
302A THR 3.5 4.9 - - - +
303A SER* 3.6 16.6 - - - +
250C PHE* 4.2 22.7 - - + -
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Residues in contact with VAL 285 (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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183A PHE* 4.0 25.8 - - + -
200A LEU* 4.0 17.5 - - + -
215A ILE* 4.7 8.5 - - + -
216A HIS 4.4 0.9 - - - -
217A MET* 4.3 24.5 - - + -
283A ILE* 4.5 2.9 - - + +
284A ILE* 1.3 75.8 - - - +
286A ILE* 1.3 63.9 + - - +
287A LEU 3.9 0.2 - - - -
300A ALA 3.6 0.7 - - - +
301A ARG* 3.3 28.6 - - - +
302A THR* 2.9 30.4 + - - +
304A TYR* 3.9 22.0 - - + -
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Residues in contact with ILE 286 (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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214A THR 3.8 0.7 - - - +
215A ILE* 3.3 6.7 - - - -
216A HIS* 2.8 61.5 + - + +
218A GLN* 4.4 8.5 - - + +
284A ILE* 3.9 35.2 - - + +
285A VAL* 1.3 76.5 - - - +
287A LEU* 1.3 58.3 + - - +
288A GLU* 3.8 21.8 + - + +
299A GLN* 3.4 22.0 - - + +
301A ARG* 5.3 1.3 - - + -
250C PHE* 4.1 33.4 - - + -
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Residues in contact with LEU 287 (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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181A LEU* 4.0 42.5 - - + +
183A PHE* 3.7 29.8 - - + -
202A VAL* 4.2 13.9 - - + -
210A ILE* 5.1 7.2 - - + -
213A ALA* 4.9 6.1 - - + +
215A ILE* 3.7 30.3 - - + -
285A VAL 3.9 0.4 - - - -
286A ILE* 1.3 70.9 - - - +
288A GLU* 1.3 72.3 + - - +
298A THR 3.9 0.3 - - - +
299A GLN* 3.2 9.5 - - - +
300A ALA* 2.9 39.3 + - + +
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Residues in contact with GLU 288 (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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210A ILE* 5.3 0.3 - - - +
213A ALA* 2.7 33.4 - - - +
214A THR* 3.1 36.9 + - - +
216A HIS* 3.5 21.2 + - - -
286A ILE* 3.9 16.5 - - + +
287A LEU* 1.3 82.5 - - - +
289A GLY* 1.3 51.2 + - - +
298A THR 3.5 9.9 - - - +
299A GLN* 3.9 16.6 - - + +
211C ILE* 3.6 9.6 - - + +
212C SER* 3.1 37.9 + - - -
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Residues in contact with GLY 289 (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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210A ILE* 4.9 4.7 - - - -
211A ILE 4.1 0.9 - - - -
212A SER 4.3 3.4 - - - -
213A ALA* 3.4 19.7 - - - -
288A GLU* 1.3 80.4 - - - +
290A VAL* 1.3 60.3 + - - -
297A THR* 3.1 11.9 - - - -
298A THR* 2.8 35.4 + - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE* 3.1 11.8 - - - +
211A ILE* 2.9 61.6 + - + +
212A SER* 4.9 3.1 + - - -
289A GLY* 1.3 72.8 - - - -
291A VAL* 1.3 74.3 + - - +
294A THR 3.5 7.9 - - - +
295A GLY* 3.2 29.2 - - - +
296A ILE 3.4 8.1 - - - +
297A THR* 3.5 13.7 - - + -
298A THR* 6.0 1.8 - - - -
297G THR* 3.9 17.7 - - - +
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Residues in contact with VAL 291 (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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174A ALA* 5.4 2.9 - - + -
177A ARG* 4.9 22.9 - - + +
209A MET 4.3 4.5 - - - -
210A ILE* 5.0 2.7 - - - -
211A ILE* 5.0 0.3 - - - +
290A VAL* 1.3 86.2 - - - +
292A GLU* 1.3 61.7 + - - +
293A THR* 3.1 7.9 - - - +
294A THR* 2.7 47.4 + - - +
295A GLY* 4.9 0.2 - - - -
296A ILE 3.5 6.8 + - - +
298A THR* 6.0 2.1 - - + +
296G ILE* 5.2 2.4 - - - +
297G THR 5.1 3.3 - - - +
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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