Contacts of the strand formed by residues 242 - 250 (chain D) in PDB entry 2C11
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 HIS 242 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228D GLY* 3.6 15.7 - - - -
229D LEU 3.7 4.7 - - - -
230D TYR* 3.6 32.0 + + + -
240D LEU 3.7 2.4 + - - -
241D HIS* 1.3 74.9 - - - +
243D VAL* 1.3 62.4 + - - +
244D GLY* 2.9 35.4 + - - -
245D LEU 3.6 9.8 + - - -
246D GLU* 3.0 46.0 + - + +
291D ILE* 4.5 6.4 - - - +
376D SER* 5.6 0.2 + - - -
378D ALA* 5.2 0.7 - - + -
497D SER* 3.7 12.3 + - - +
498D ALA* 3.7 10.7 - - + +
499D PHE* 3.7 34.6 + - - +
514D HIS 5.0 1.9 - - - +
515D THR* 4.9 3.0 - - + +
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Residues in contact with VAL 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 6.3 1.1 - - + -
199D CYS* 4.1 20.5 - - - -
208D LEU* 4.1 24.0 - - + -
229D LEU* 2.9 45.1 + - + +
230D TYR* 4.2 0.2 - - - -
231D TYR* 3.7 36.3 - - + +
241D HIS 4.0 1.8 - - - +
242D HIS* 1.3 70.8 - - - +
244D GLY* 1.3 58.0 + - - +
245D LEU* 3.8 14.4 - - + +
266D TYR* 4.2 4.9 - - + -
267D GLN* 3.9 11.8 + - - -
291D ILE* 3.8 23.7 - - + +
499D PHE* 4.7 0.9 - - - -
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Residues in contact with GLY 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D HIS* 2.9 18.7 - - - -
243D VAL* 1.3 79.0 - - - +
245D LEU* 1.3 59.0 + - - +
246D GLU* 4.3 1.8 - - - -
265D PHE* 3.6 4.8 - - - +
266D TYR* 3.1 7.7 - - - -
267D GLN* 2.6 31.8 + - - -
499D PHE* 3.5 23.1 - - - -
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.2 11.0 - - + -
195D LEU* 4.8 14.4 - - + -
228D GLY* 3.5 0.5 - - - -
229D LEU* 3.0 54.4 + - + +
242D HIS* 3.6 2.4 + - - -
243D VAL* 3.8 13.3 - - + +
244D GLY* 1.3 79.4 - - - +
246D GLU* 1.3 61.6 + - - +
247D LEU* 3.6 15.5 - - + -
264D VAL* 3.4 25.6 - - + -
265D PHE 3.2 14.6 - - - +
266D TYR* 3.8 23.3 - - + -
274D LEU* 4.8 5.4 - - + -
277D LEU* 4.2 7.6 - - + -
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D TRP* 3.2 17.3 - - + -
227D PHE 3.2 8.3 - - - +
228D GLY* 3.9 3.8 - - - -
242D HIS* 3.0 36.9 - - + +
244D GLY 5.1 0.2 - - - -
245D LEU* 1.3 75.0 - - - +
247D LEU* 1.3 64.5 + - - +
265D PHE* 2.8 39.2 + - + +
376D SER* 3.1 17.7 + - - -
377D PRO* 3.1 19.6 - - - +
378D ALA* 2.9 44.7 + - + +
379D ALA 4.5 0.3 + - - -
498D ALA* 4.6 2.4 - - - +
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ILE* 4.0 36.6 - - + -
187D GLU* 5.1 0.2 - - + -
188D LEU* 4.5 7.9 - - + -
225D THR 3.2 4.2 - - - +
226D TRP* 3.6 3.8 - - - -
227D PHE* 2.7 40.3 + - + +
229D LEU* 4.5 6.5 - - + -
245D LEU* 3.6 24.2 - - + -
246D GLU* 1.3 82.4 - - - +
248D LEU* 1.3 59.7 - - - +
249D VAL* 3.4 3.7 + - + -
261D ILE* 4.2 23.6 - - + -
263D LYS 3.8 3.1 - - - +
264D VAL* 3.6 22.7 - - + -
274D LEU* 3.7 17.0 - - + -
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C TRP* 4.2 21.3 - - + +
217D GLY* 5.8 0.7 - - - -
224D ALA* 3.6 35.2 - - + +
225D THR 3.4 2.2 - - - -
226D TRP* 3.4 46.0 - - + +
247D LEU* 1.3 70.2 - - - +
249D VAL* 1.3 59.8 + - - +
261D ILE* 3.4 5.3 - - - -
262D GLN* 2.8 63.5 + - + +
263D LYS* 3.0 24.0 + - + +
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ILE* 4.2 23.6 - - + -
182D MET* 4.7 13.5 - - + -
183D ILE* 4.3 11.7 - - + -
224D ALA* 2.9 6.0 - - - -
225D THR 2.7 41.4 + - - +
227D PHE* 3.9 20.6 - - + -
247D LEU 4.3 3.8 - - - +
248D LEU* 1.3 75.0 - - - +
250D ASN* 1.3 62.7 + - - +
251D HIS* 3.3 26.8 - - + +
259D TRP* 5.1 1.1 - - + -
260D THR 3.4 7.6 - - - +
261D ILE* 3.9 20.4 - - + -
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Residues in contact with ASN 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ARG 3.9 6.5 + - - +
224D ALA* 4.2 4.9 - - - +
248D LEU 3.9 0.6 + - - -
249D VAL* 1.3 71.2 - - - +
251D HIS* 1.3 60.2 + - - +
252D LYS* 3.6 21.0 + - - +
258D ARG 4.5 1.2 - - - +
259D TRP* 3.3 8.0 - - - -
260D THR* 2.7 45.3 + - - +
262D GLN* 2.7 40.1 + - + +
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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