Contacts of the strand formed by residues 309 - 316 (chain A) in PDB entry 2D2I
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 LEU 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL* 3.6 31.0 - - + -
249A VAL 3.6 17.3 - - - +
250A GLN* 4.0 11.4 - - + +
303A LEU* 3.9 1.6 - - + +
304A VAL* 3.4 1.6 - - - -
305A MET* 2.8 52.4 + - + +
307A GLY 3.7 0.8 - - - -
308A ASP* 1.3 80.9 + - - +
310A VAL* 1.3 64.1 + - - +
311A LYS* 5.5 1.3 - - + -
175B LYS* 3.6 23.8 - - + +
176B GLY* 5.6 3.4 - - - -
177B THR* 4.7 14.8 - - + +
248B VAL* 5.7 0.9 - - + -
250B GLN* 5.7 5.6 - - + +
309B LEU* 4.9 14.1 - - + -
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Residues in contact with VAL 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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167A LEU* 4.5 8.7 - - + -
171A PHE* 6.1 1.3 - - + -
247A LEU 3.5 0.9 - - - +
248A VAL* 3.1 5.4 - - - +
249A VAL* 2.9 59.3 + - + -
251A VAL* 4.1 18.6 - - + -
255A THR* 4.2 16.4 - - + -
260A VAL* 4.5 10.3 - - + -
303A LEU 3.3 7.0 - - - +
304A VAL* 4.0 19.5 - - + -
308A ASP 4.5 0.9 - - - -
309A LEU* 1.3 83.3 - - - +
311A LYS* 1.3 62.4 + - - +
312A VAL* 4.1 18.2 - - + -
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Residues in contact with LYS 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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246A ASP* 3.4 26.0 + - - +
247A LEU 3.1 2.7 - - - -
248A VAL* 3.9 11.2 - - + +
301A LEU 4.3 5.1 - - - +
302A THR* 3.4 5.2 - - - +
303A LEU* 2.7 58.6 + - + +
309A LEU* 5.5 1.6 - - + -
310A VAL* 1.3 75.8 - - - +
312A VAL* 1.3 66.5 + - - +
313A ILE* 4.3 11.7 - - + -
177B THR* 3.2 40.7 + - + +
178B MET* 4.0 10.6 + - - +
179B THR* 3.2 28.0 + - - -
232B GLY* 5.1 0.2 - - - -
233B ILE* 4.3 11.9 - - + +
246B ASP 5.6 0.2 + - - -
248B VAL* 6.1 0.2 - - - +
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 3.6 32.3 - - + -
167A LEU* 3.7 23.8 - - + -
245A VAL* 3.7 2.6 - - + +
246A ASP* 3.8 0.5 - - - -
247A LEU* 3.0 35.8 + - + +
260A VAL* 4.8 1.3 - - + -
264A LEU* 4.4 21.1 - - + -
297A VAL* 5.1 4.5 - - + -
302A THR* 4.6 15.7 - - + +
310A VAL* 4.1 11.7 - - + -
311A LYS* 1.3 80.6 - - - +
313A ILE* 1.3 68.2 + - - +
314A ALA* 5.0 1.8 - - + +
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Residues in contact with ILE 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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244A VAL* 3.1 31.2 - - + -
245A VAL 3.2 2.9 - - - +
246A ASP* 3.4 38.8 - - + +
297A VAL* 3.6 3.3 - - - +
298A ASP* 2.9 32.7 + - + +
301A LEU* 3.9 38.7 + - + +
302A THR* 5.3 0.6 + - - +
311A LYS* 4.3 6.7 - - + -
312A VAL* 1.3 76.2 - - - +
314A ALA* 1.3 62.4 + - - +
315A TRP* 5.3 1.8 - - + +
179B THR* 5.9 0.4 - - + -
233B ILE* 3.7 28.9 - - + -
235B LEU* 5.4 6.7 - - + -
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Residues in contact with ALA 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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159A CYS* 3.7 21.7 - - - -
163A VAL* 4.3 19.3 - - + -
244A VAL* 3.3 3.9 - - - -
245A VAL* 2.6 47.3 + - + +
296A ILE 3.1 17.7 - - - +
297A VAL* 4.2 5.2 - - + +
312A VAL* 4.1 3.5 + - + -
313A ILE* 1.3 75.1 - - - +
315A TRP* 1.3 60.3 + - - +
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Residues in contact with TRP 315 (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* 4.6 3.6 - - + -
243A SER 3.5 23.3 - - - -
244A VAL* 3.5 21.7 - - + +
283A LEU 4.4 3.4 - - - -
285A SER* 3.4 33.0 - - - -
288A PHE* 3.2 39.9 - + + -
295A SER* 3.7 1.7 - - - -
296A ILE* 2.7 49.4 + - + +
298A ASP* 2.9 32.7 + - + +
301A LEU* 5.3 1.2 - - + +
313A ILE* 5.5 1.1 - - + -
314A ALA* 1.3 76.2 - - - +
316A TYR* 1.3 64.7 + - - +
199B ARG* 4.4 0.2 - - - +
208B ILE* 3.4 41.5 - - + -
210B PRO* 3.2 28.5 - - + -
235B LEU* 5.0 1.6 - - + -
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Residues in contact with TYR 316 (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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155A CYS* 3.7 35.0 - - + -
156A THR* 2.7 30.9 + - - +
159A CYS* 3.5 18.2 - - + -
180A THR* 2.8 16.5 + - - -
182A HIS* 3.3 5.4 - + - -
242A VAL* 3.2 3.5 - - - -
243A SER* 2.8 45.7 + - - -
244A VAL 3.8 15.0 - - - -
245A VAL* 3.6 20.9 - - + -
288A PHE* 5.7 1.3 - - - -
293A GLU 5.1 1.8 - - - +
294A SER* 3.4 20.4 - - - +
296A ILE* 4.1 8.7 - - - +
314A ALA 3.9 1.1 - - - -
315A TRP* 1.3 79.4 - - - +
317A ASP* 1.3 61.7 + - - +
318A ASN* 3.1 24.3 + - + -
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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