Contacts of the strand formed by residues 306 - 311 (chain A) in PDB entry 2WEA
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 GLN 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A VAL 4.0 4.7 - - - +
263A TYR* 2.6 36.2 + - - -
265A ALA* 3.7 26.1 - - - +
266A THR 3.8 8.5 + - - +
302A PHE* 3.9 24.7 - - + +
303A LEU 2.9 10.7 + - - +
304A LYS 3.4 0.2 - - - -
305A SER* 1.3 110.0 + - - +
307A TYR* 1.3 61.5 + - - +
308A VAL* 3.8 18.8 + - + +
319A PHE* 4.0 3.9 - - + +
320A ALA 3.3 12.2 + - - +
321A PRO* 4.8 1.0 - - - +
322A GLN* 2.7 26.9 + - - +
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Residues in contact with TYR 307 (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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154A ALA* 3.2 29.9 - - + +
155A VAL 3.6 20.0 - - - -
156A ALA* 4.0 7.9 - - + -
164A VAL* 4.8 0.4 - - + -
166A ASP* 2.7 27.8 + - - -
170A ILE* 3.9 5.0 - - + -
171A ASP 3.0 20.5 + - - -
174A LYS* 3.4 38.8 - - + +
175A TYR* 3.2 42.4 - + + -
179A LEU* 4.4 2.3 - - + +
306A GLN* 1.3 74.9 - - - +
308A VAL* 1.3 61.1 + - - +
309A VAL* 3.8 15.7 - - + -
318A GLY 3.6 0.5 - - - +
319A PHE* 3.5 5.9 - - - -
320A ALA 2.9 26.3 + - - -
322A GLN* 4.1 2.5 - - + +
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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
----------------------------------------------------------
154A ALA* 3.1 3.4 - - - -
155A VAL* 2.9 37.9 + - + +
212A ALA* 4.9 3.1 - - + -
303A LEU* 3.9 22.4 - - + -
306A GLN* 3.8 21.3 - - + +
307A TYR* 1.3 78.6 - - - +
309A VAL* 1.3 64.0 + - - +
310A PHE* 3.6 29.5 - - + -
317A LEU* 3.8 19.3 - - + -
318A GLY 3.2 8.3 - - - +
319A PHE* 3.8 21.5 - - + -
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Residues in contact with VAL 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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152A LEU* 4.4 9.4 - - + -
153A PHE 3.7 8.5 - - - +
154A ALA* 3.9 4.7 - - + -
170A ILE* 4.1 18.4 - - + -
179A LEU* 3.8 24.7 - - + -
181A TYR* 4.1 17.7 - - + +
307A TYR* 3.8 28.5 - - + -
308A VAL* 1.3 71.6 - - - +
310A PHE* 1.3 67.6 + - - +
311A ASP* 3.7 7.2 + - + +
317A LEU* 3.1 10.2 - - - +
318A GLY* 2.8 42.4 + - - +
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Residues in contact with PHE 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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34A THR* 3.8 28.7 - - + -
141A PHE* 4.6 0.5 - - - -
152A LEU* 3.2 5.1 - - - -
153A PHE* 2.7 72.8 + + + +
154A ALA* 4.6 0.2 - - - -
155A VAL* 3.5 29.2 - - + -
191A TRP* 3.5 39.0 - + + -
212A ALA* 3.7 32.8 - - + -
214A THR* 4.8 3.6 - - + -
303A LEU* 5.2 2.9 - - + -
308A VAL* 3.6 22.2 - - + -
309A VAL* 1.3 70.1 - - - +
311A ASP* 1.3 61.1 + - - +
312A SER 3.9 0.5 + - - -
317A LEU* 3.6 6.5 - - + -
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Residues in contact with ASP 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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151A PRO* 3.7 8.7 - - - +
152A LEU* 3.8 23.1 - - + +
181A TYR* 4.5 5.3 + - + -
191A TRP* 3.6 3.1 - - - -
309A VAL* 4.4 9.0 - - + -
310A PHE* 1.3 72.9 - - - +
312A SER* 1.3 63.5 + - - +
313A ASP* 3.0 31.6 + - - +
315A PRO* 3.3 4.0 - - - +
316A GLN* 2.9 70.0 + - + +
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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