Contacts of the strand formed by residues 241 - 250 (chain P) in PDB entry 3HAE
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 241 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30P ASP* 4.1 29.4 - - + -
207P SER* 2.9 14.7 + - - -
208P PHE* 2.8 58.8 + - + +
209P TYR* 4.1 9.0 - + - -
211P ALA* 3.6 29.6 - - + -
233P THR* 4.0 11.0 - - + -
234P ARG 3.1 22.4 - - - +
235P PRO* 3.6 23.3 - - + -
236P ALA 4.2 0.7 - - - +
239P GLY* 4.0 15.3 - - - -
240P THR* 1.3 77.9 - - - +
242P GLN* 1.3 64.4 + - - +
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Residues in contact with GLN 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204P TRP* 5.3 1.1 - - + -
205P ALA 3.3 6.3 - - - -
206P LEU* 3.9 26.4 - - + +
207P SER 4.6 2.7 - - - +
208P PHE* 3.7 2.7 - - - -
233P THR* 3.4 3.5 - - - +
234P ARG* 2.9 77.8 + - + +
236P ALA* 3.8 16.6 - - + +
241P PHE* 1.3 79.5 - - - +
243P LYS* 1.3 62.7 + - - +
10Q TYR* 3.3 15.4 - - - -
11Q SER 3.8 6.9 + - - +
12Q ARG 3.4 21.8 - - - +
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Residues in contact with LYS 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204P TRP* 3.9 3.8 - - - -
205P ALA* 3.0 31.9 + - + +
208P PHE* 4.3 8.5 - - + -
213P ILE* 3.5 27.1 - - + -
215P LEU* 4.0 18.8 - - + +
230P LEU* 4.4 24.0 - - - +
231P VAL* 2.6 38.8 + - - +
232P GLU* 3.8 2.6 - - - +
233P THR* 3.1 32.1 + - - +
234P ARG* 5.8 1.8 - - - +
242P GLN* 1.3 76.2 - - - +
244P TRP* 1.3 69.4 + - - +
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Residues in contact with TRP 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202P ARG* 3.4 37.7 - - + +
203P CYS 3.2 13.0 - - - +
204P TRP* 3.4 43.3 - + + -
215P LEU* 3.8 5.6 - - - -
229P GLU* 3.8 42.6 - - + -
230P LEU* 3.7 4.6 - - - +
231P VAL* 3.3 56.5 + - + +
234P ARG* 3.9 15.8 - - - +
243P LYS* 1.3 79.5 - - - +
245P ALA* 1.3 67.9 + - - +
246P ALA* 3.9 8.3 - - + -
8Q GLN* 4.6 0.4 + - - -
99Q MET* 4.7 16.5 - - - +
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Residues in contact with ALA 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202P ARG* 3.3 1.7 - - - +
203P CYS* 2.7 40.6 + - + +
215P LEU* 3.8 17.2 - - + +
217P TRP* 3.4 24.8 + - + +
228P THR* 6.2 0.4 - - + -
229P GLU 3.4 6.1 - - - +
230P LEU* 3.7 22.2 - - + -
244P TRP* 1.3 76.7 - - - +
246P ALA* 1.3 60.3 + - - +
259P CYS* 5.0 0.7 - - - -
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Residues in contact with ALA 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200P THR* 3.9 16.8 - - + -
201P LEU 3.1 10.8 - - - +
202P ARG* 3.8 25.4 - - - +
217P TRP* 3.6 3.3 + - - +
228P THR* 3.2 8.0 + - - -
229P GLU* 2.7 40.6 + - + +
244P TRP* 3.9 8.5 - - + -
245P ALA* 1.3 77.6 - - - +
247P VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P ALA 3.6 0.3 - - - +
200P THR* 3.2 5.4 - - - -
201P LEU* 2.8 33.3 + - + +
217P TRP* 3.2 49.8 - - + +
224P GLN* 4.4 16.2 - - + -
226P GLN 4.2 8.1 - - - +
227P ASP* 3.2 19.7 - - + +
228P THR* 4.4 3.4 - - - +
246P ALA* 1.3 71.5 - - - +
248P VAL* 1.3 70.5 + - - +
249P VAL* 4.0 13.4 + - + -
257P TYR* 4.5 8.3 - - + -
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Residues in contact with VAL 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P VAL* 5.1 8.3 - - + -
198P GLU* 4.4 26.0 - - + +
199P ALA 3.2 8.3 - - - +
200P THR* 4.1 20.0 - - + +
227P ASP* 3.2 41.7 + - + +
247P VAL* 1.3 82.7 - - - +
249P VAL* 1.3 63.5 + - - +
250P PRO* 4.5 2.8 - - - +
257P TYR* 5.1 1.2 + - - -
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Residues in contact with VAL 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198P GLU* 3.3 6.5 - - - -
199P ALA* 2.7 51.2 + - + +
201P LEU* 4.5 11.2 - - + -
247P VAL* 4.1 12.3 - - + +
248P VAL* 1.3 79.7 - - - +
250P PRO* 1.4 77.9 - - + +
254P GLU* 4.2 30.1 - - + +
257P TYR* 3.6 43.5 - - + -
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Residues in contact with PRO 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197P HIS 3.6 10.8 - - - +
198P GLU* 4.5 5.1 - - + -
248P VAL 4.5 2.5 - - - +
249P VAL* 1.4 88.7 - - + +
251P SER* 1.3 66.9 + - - +
253P GLN* 3.0 58.3 + - + +
257P TYR* 3.9 9.4 - - - +
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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