Contacts of the strand formed by residues 331 - 338 (chain A) in PDB entry 1W5A
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 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLU* 3.0 24.4 - - - +
256A SER 2.9 14.1 + - - +
261A ARG* 3.2 48.5 - - + +
262A ALA* 4.4 17.9 - - + -
265A ALA* 3.7 7.4 - - + +
289A VAL* 4.1 16.8 - - + -
290A MET 3.3 8.7 - - - +
291A GLY* 4.2 4.3 - - - -
292A PRO* 4.1 7.6 - - + -
295A LEU* 4.4 8.1 - - + -
299A GLU* 4.2 4.0 - - - +
329A ASN 4.2 0.2 + - - -
330A THR* 1.3 75.1 - - - +
332A ARG* 1.3 68.7 + - - +
333A VAL* 4.5 1.3 - - + -
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Residues in contact with ARG 332 (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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217A ASN* 3.6 32.0 + - - +
253A ILE* 4.8 12.2 - - + +
254A GLY 3.5 8.1 - - - +
255A GLU* 3.2 28.1 + - + +
288A HIS 3.7 0.7 - - - +
289A VAL* 3.6 0.2 - - - -
290A MET* 2.6 73.3 + - + +
324A ASP* 4.1 8.5 + - - -
327A LEU* 3.9 31.5 - - + +
330A THR* 4.2 2.3 + - + +
331A VAL* 1.3 74.2 - - - +
333A VAL* 1.3 72.7 + - - +
334A LEU* 5.8 0.4 - - + -
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A GLY 3.6 0.9 - - - +
253A ILE* 3.5 7.6 - - - +
254A GLY 2.7 33.1 + - - +
265A ALA* 3.6 22.2 - - + +
266A VAL* 3.9 12.3 - - - +
269A ALA* 4.0 6.6 - - + +
287A ILE* 4.5 3.4 - - + -
288A HIS 3.6 3.1 - - - +
289A VAL* 4.6 4.5 - - + -
303A VAL* 3.9 33.2 - - + -
331A VAL* 4.5 5.4 - - + -
332A ARG* 1.3 82.9 - - - +
334A LEU* 1.3 62.5 + - - +
335A LEU* 3.4 29.4 - - + -
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Residues in contact with LEU 334 (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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217A ASN* 3.8 8.5 - - + +
218A ALA* 3.8 19.5 - - - +
221A GLY* 3.6 37.7 - - - +
222A LEU* 3.7 6.5 - - - +
225A LEU* 6.5 0.2 - - + -
251A ILE* 4.3 9.0 - - + -
252A GLY 3.6 7.2 - - - +
253A ILE* 4.1 17.3 - - + +
286A LEU 3.8 0.7 - - - +
287A ILE* 3.6 5.2 - - - +
288A HIS* 3.0 40.3 + - + +
290A MET* 4.0 13.2 - - + +
332A ARG* 5.8 0.2 - - + -
333A VAL* 1.3 72.8 - - - +
335A LEU* 1.3 73.0 + - - +
336A VAL* 4.2 15.3 - - + -
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Residues in contact with LEU 335 (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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250A MET 4.5 0.2 - - - -
251A ILE* 3.0 11.5 - - - +
252A GLY 2.8 42.8 + - - +
266A VAL* 4.6 0.7 - - + +
269A ALA* 3.7 19.3 - - + +
270A LEU* 3.6 37.9 - - + +
275A LEU* 4.7 5.2 - - + -
286A LEU 3.9 1.3 - - - -
287A ILE* 3.8 19.5 - - + -
307A VAL* 3.9 19.1 - - + -
333A VAL* 3.4 28.9 - - + -
334A LEU* 1.3 75.0 - - - +
336A VAL* 1.3 64.1 + - - +
337A ILE* 4.1 13.5 - - + -
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Residues in contact with VAL 336 (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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186A THR* 5.7 0.7 - - + -
188A VAL* 4.3 15.0 - - + -
222A LEU* 4.3 21.8 - - + -
249A ALA* 4.2 19.7 - - + -
250A MET 3.5 4.5 - - - +
251A ILE* 4.3 9.6 - - + -
285A ALA* 3.1 8.0 - - - +
286A LEU* 3.0 58.8 + - + +
334A LEU* 4.2 17.0 - - + -
335A LEU* 1.3 80.1 - - - +
337A ILE* 1.3 62.7 + - - +
338A THR* 3.8 3.1 + - + +
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Residues in contact with ILE 337 (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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249A ALA* 3.1 4.7 - - - -
250A MET* 2.9 34.8 + - + +
270A LEU* 5.8 0.4 - - + -
275A LEU* 4.2 17.7 - - + -
277A VAL* 6.1 0.2 - - + -
279A ILE* 4.0 25.1 - - + -
282A ALA* 3.2 34.5 - - + -
284A GLY 3.7 2.0 - - - +
285A ALA* 3.7 17.5 - - + -
307A VAL* 4.8 4.5 - - + -
311A LEU* 4.4 12.6 - - + -
335A LEU* 4.6 15.7 - - + -
336A VAL* 1.3 82.7 - - - +
338A THR* 1.3 60.8 + - - +
340A VAL* 3.7 16.9 - - + +
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Residues in contact with THR 338 (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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186A THR* 4.3 13.7 - - + +
242A VAL* 4.3 12.4 - - + +
243A MET* 5.8 0.4 - - - -
246A GLY* 3.5 17.6 - - - -
249A ALA* 3.8 16.4 - - + -
282A ALA* 3.7 2.4 - - - -
283A THR* 3.3 23.4 + - - +
284A GLY* 3.1 28.1 + - - +
285A ALA 4.1 0.2 + - - -
286A LEU* 4.4 22.2 - - + -
336A VAL* 4.5 4.5 - - + +
337A ILE* 1.3 76.4 - - - +
339A GLY* 1.3 66.5 + - - +
340A VAL* 3.4 8.1 + - - +
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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