Contacts of the strand formed by residues 307 - 314 (chain A) in PDB entry 4WNC
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 PHE 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A THR* 3.7 30.5 - - + -
247A CYS 3.5 13.9 - - - -
248A ARG* 3.6 26.2 - - + -
303A LEU* 2.9 54.3 + - + +
304A ASN* 3.1 24.1 + - - +
305A ASP 3.7 0.2 - - - -
306A HIS* 1.3 79.2 - - + +
308A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 308 (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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245A LEU 3.6 0.7 - - - +
246A THR* 3.4 6.3 - - - +
247A CYS* 3.0 51.6 + - - +
249A LEU* 4.2 17.5 - - + -
253A ALA 4.7 4.3 - - - +
255A TYR* 5.2 0.7 - - + -
258A ILE* 4.1 17.3 - - + -
301A ILE 3.7 7.2 - - - +
302A ALA* 3.7 19.7 - - + -
303A LEU 4.7 0.2 - - - +
304A ASN 3.9 6.7 - - - +
306A HIS 5.0 0.2 - - - -
307A PHE* 1.3 82.5 - - - +
309A LYS* 1.3 59.9 + - - +
310A LEU* 4.0 23.8 - - + -
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Residues in contact with LYS 309 (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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244A ASP* 2.9 42.5 + - - +
245A LEU 3.3 3.6 - - - +
246A THR* 2.8 30.3 + - + +
299A ALA 6.0 0.7 - - - +
300A GLY* 3.2 6.5 - - - -
301A ILE* 2.8 55.3 + - + +
308A VAL* 1.3 73.6 - - - +
310A LEU* 1.3 65.1 + - - +
311A ILE* 4.1 8.5 - - + -
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Residues in contact with LEU 310 (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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160A LEU* 4.2 15.3 - - + +
164A ILE* 3.7 37.0 - - + -
243A VAL* 3.6 1.4 - - - +
244A ASP* 3.5 3.6 - - - -
245A LEU* 2.7 42.4 + - + +
247A CYS* 4.5 9.9 - - - -
255A TYR* 3.9 20.2 - - + -
258A ILE* 4.1 9.0 - - + -
295A PHE* 3.9 26.2 - - + -
300A GLY* 4.7 0.9 - - - -
308A VAL* 4.0 26.7 - - + -
309A LYS* 1.3 81.9 - - - +
311A ILE* 1.3 62.2 + - - +
312A SER 4.3 0.2 + - - -
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Residues in contact with ILE 311 (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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242A VAL* 3.6 22.9 - - + -
243A VAL 3.3 1.6 - - - -
244A ASP* 3.7 32.1 - - + +
295A PHE* 3.6 9.1 - - - -
296A ASP* 2.9 36.2 + - + +
299A ALA* 3.9 26.9 - - + +
300A GLY* 3.9 24.2 - - - +
309A LYS* 4.1 9.9 - - + -
310A LEU* 1.3 84.2 - - - +
312A SER* 1.3 66.2 + - - +
313A TRP* 4.4 5.8 - - + +
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Residues in contact with SER 312 (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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156A CYS* 3.7 9.8 - - - -
160A LEU* 4.1 18.6 - - - -
242A VAL* 3.3 5.3 - - - +
243A VAL* 2.8 42.3 + - - +
274A LEU* 4.9 0.2 - - - +
293A SER* 2.5 29.9 + - - -
294A THR 3.1 22.8 + - - -
295A PHE* 3.6 2.3 + - - -
296A ASP 4.5 0.2 - - - +
310A LEU 4.3 0.4 + - - -
311A ILE* 1.3 76.5 - - - +
313A TRP* 1.3 59.7 + - - +
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Residues in contact with TRP 313 (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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240A VAL* 4.2 5.2 - - + -
241A SER* 3.6 10.8 - - - -
242A VAL* 3.6 36.8 - - + -
281A VAL* 3.8 14.9 - - + +
282A VAL* 4.3 1.8 - - - -
283A SER* 3.5 41.7 - - - -
286A PHE* 3.3 45.4 - + + -
291A HIS* 6.0 0.2 - - - +
293A SER* 3.5 3.6 + - - -
294A THR* 2.8 36.0 + - - +
296A ASP* 2.9 42.7 + - + +
299A ALA* 6.0 0.7 - - + -
311A ILE* 4.4 4.7 - - + +
312A SER* 1.3 75.0 - - - +
314A TYR* 1.3 65.4 + - - +
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Residues in contact with TYR 314 (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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152A CYS* 3.7 30.3 - - + -
153A THR* 2.7 28.7 + - - +
156A CYS* 3.4 17.0 - - + -
177A THR* 2.8 16.6 + - - -
179A HIS* 3.3 7.8 - + - -
240A VAL* 4.2 4.5 - - - +
241A SER* 2.8 64.4 + - - +
242A VAL* 3.7 10.3 - - - -
243A VAL* 3.8 18.8 - - + -
286A PHE* 5.2 1.8 - - - -
291A HIS 5.1 2.5 - - - +
292A SER 3.4 22.0 - - - +
313A TRP* 1.3 76.2 - - - +
315A ASP* 1.3 61.2 + - - +
316A ASN* 3.1 25.9 + - + -
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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