Contacts of the strand formed by residues 247 - 256 (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 GLY 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A LYS* 5.3 7.9 - - - -
184A THR* 5.2 0.7 + - - -
185A ASP 3.1 9.4 + - - -
186A THR* 3.4 1.9 - - - -
187A LEU* 2.7 35.6 + - - +
245A ASN 3.1 5.6 - - - -
246A GLY* 1.3 75.5 - - - +
248A LEU* 1.3 54.6 + - - -
249A ALA 3.9 0.2 + - - -
341A GLN* 3.9 17.7 - - - -
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Residues in contact with LEU 248 (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 LYS* 4.6 7.3 - - - +
187A LEU* 3.3 30.1 - - + +
189A VAL* 3.4 23.6 - - + -
246A GLY 3.3 0.8 + - - -
247A GLY* 1.3 71.9 - - - -
249A ALA* 1.3 64.6 + - - +
250A MET* 4.5 11.0 - - + -
339A GLY 3.2 6.4 + - - -
340A VAL* 3.2 42.9 + - + +
341A GLN* 3.3 28.3 + - + -
344A ILE* 4.5 18.2 - - + -
346A PHE* 4.4 22.2 - - + -
351A LEU* 5.3 4.5 - - + -
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Residues in contact with ALA 249 (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* 4.0 15.5 - - + -
187A LEU 2.9 7.5 + - - +
188A VAL* 3.2 14.4 - - + -
189A VAL* 2.8 27.5 + - - +
248A LEU* 1.3 75.4 - - - +
250A MET* 1.3 69.1 + - - +
336A VAL* 4.2 5.2 - - + -
337A ILE 3.1 15.7 - - - +
338A THR* 3.8 20.9 - - + -
340A VAL* 4.4 0.7 - - - -
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Residues in contact with MET 250 (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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188A VAL* 4.6 0.4 - - - -
189A VAL* 3.7 15.5 - - + +
191A PRO* 4.0 20.6 - - + -
248A LEU* 4.5 9.6 - - + -
249A ALA* 1.3 79.5 - - - +
251A ILE* 1.3 67.6 + - - +
274A LEU 3.4 26.5 - - - +
275A LEU* 4.6 9.0 - - + -
276A ASP* 3.7 24.5 - - + +
277A VAL* 3.8 26.5 - - + -
336A VAL* 3.5 2.1 - - - -
337A ILE* 2.9 35.9 + - + +
340A VAL* 4.6 4.9 - - + +
344A ILE* 4.3 15.5 - - + -
351A LEU* 4.7 10.8 - - + -
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Residues in contact with ILE 251 (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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188A VAL* 3.4 29.6 - - + -
189A VAL 4.7 1.8 + - - -
190A ILE* 4.0 20.4 - - + -
214A VAL* 4.0 8.1 - - + -
218A ALA* 3.8 29.8 - - + -
222A LEU* 6.2 0.9 - - + -
250A MET* 1.3 76.8 - - - +
252A GLY* 1.3 59.9 + - - +
253A ILE* 4.0 25.4 - - + -
274A LEU* 3.2 19.1 + - + +
275A LEU* 3.1 29.9 + - - +
334A LEU* 4.3 6.1 - - + -
335A LEU 3.0 13.7 - - - +
336A VAL* 4.3 11.4 - - + -
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Residues in contact with GLY 252 (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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251A ILE* 1.3 75.3 - - - +
253A ILE* 1.3 67.0 + - - +
269A ALA* 3.4 25.1 - - - -
272A SER* 3.7 7.9 - - - -
275A LEU* 4.3 3.1 - - - +
333A VAL 3.6 1.4 - - - +
334A LEU* 3.9 0.3 - - - +
335A LEU* 2.8 38.3 + - - +
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Residues in contact with ILE 253 (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 ILE* 6.0 2.6 - - + +
214A VAL* 4.1 22.2 - - + +
217A ASN* 4.2 24.0 - - + -
251A ILE* 4.0 25.8 - - + -
252A GLY* 1.3 80.2 - - - +
254A GLY* 1.3 67.1 + - - +
255A GLU* 6.0 2.2 - - + +
268A MET* 3.7 14.9 - - + +
269A ALA* 3.7 10.6 + - - -
272A SER* 3.8 15.5 + - - +
274A LEU* 4.5 8.5 - - + -
332A ARG* 4.8 15.9 - - + +
333A VAL 3.5 6.7 - - - +
334A LEU* 4.1 11.2 - - + -
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Residues in contact with GLY 254 (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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253A ILE* 1.3 79.4 - - - +
255A GLU* 1.3 61.2 + - - +
265A ALA* 3.4 24.7 - - - +
268A MET* 3.5 14.8 - - - -
269A ALA* 3.9 1.4 - - - +
332A ARG* 3.5 1.6 - - - +
333A VAL* 2.7 36.6 + - - +
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Residues in contact with GLU 255 (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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253A ILE* 6.0 2.1 - - + +
254A GLY* 1.3 75.2 - - - +
256A SER* 1.3 63.7 + - - +
265A ALA* 3.8 5.0 - - - +
268A MET* 3.6 26.2 - - + +
330A THR* 3.7 20.2 + - + +
331A VAL 3.0 17.3 - - - +
332A ARG* 3.2 40.0 + - + -
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Residues in contact with SER 256 (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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255A GLU* 1.3 78.0 - - - +
257A ASP* 1.3 62.0 + - - +
258A SER* 3.2 13.3 + - - -
261A ARG* 3.4 28.6 - - - +
264A GLU* 3.0 36.3 + - - +
265A ALA* 3.9 2.1 - - - +
330A THR* 3.8 4.2 - - - +
331A VAL 2.9 28.3 + - - +
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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