Contacts of the helix formed by residues 243 - 253 (chain B) in PDB entry 2H1H
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 SER 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A GLN* 6.1 4.5 - - - -
43B GLN* 3.2 22.2 + - - -
242B MET* 1.3 79.2 - - - +
244B LEU* 1.3 64.2 + - - +
245B GLU* 3.2 6.6 + - - +
246B GLY* 3.1 18.0 + - - +
247B VAL* 3.1 11.3 + - - +
400B AFH 3.9 2.5 - - - -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B MET* 3.9 23.6 - - + -
40B GLY 4.0 19.5 - - - +
41B PHE* 4.5 3.1 - - - -
43B GLN* 4.0 16.3 - - + +
44B ILE* 4.1 22.9 - - + -
47B TRP* 3.7 12.1 - - + -
243B SER* 1.3 75.0 - - - +
245B GLU* 1.3 60.4 + - - +
247B VAL* 3.2 19.6 - - + +
248B ALA* 3.3 10.7 + - - +
264B LEU* 3.6 31.4 - - + -
267B LEU* 4.1 7.2 - - + -
400B AFH 3.7 14.5 + - - +
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A PRO* 4.0 12.9 - - - +
311A ALA* 5.6 5.7 - - - +
43B GLN* 2.5 40.0 - - - +
46B SER* 5.3 0.9 + - - -
47B TRP* 3.4 28.4 + - + +
168B HIS* 3.6 15.9 + - - -
169B PHE* 3.5 12.6 - - + -
243B SER* 3.1 3.4 + - - +
244B LEU* 1.3 76.2 - - - +
246B GLY* 1.3 64.8 + - - +
248B ALA* 3.2 2.6 + - - +
249B ARG* 3.1 41.4 + - - +
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Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B MET* 3.7 18.3 - - - +
243B SER* 3.1 16.6 + - - -
245B GLU* 1.3 78.4 - - - +
247B VAL* 1.3 61.3 + - - +
249B ARG* 3.2 25.2 + - - +
250B VAL* 3.3 15.6 + - - +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B VAL* 6.2 0.4 - - + -
184B LEU* 5.3 0.2 - - + -
216B PRO* 3.9 30.1 - - + -
239B LEU* 5.0 1.8 - - + -
242B MET* 3.4 18.6 - - + +
243B SER 3.1 13.8 + - - +
244B LEU* 3.2 30.7 - - + +
246B GLY* 1.3 75.7 - - - +
248B ALA* 1.3 60.4 + - - +
250B VAL* 3.4 2.4 + - + +
251B LEU* 3.0 32.8 + - + +
264B LEU* 4.2 23.8 - - + -
267B LEU* 4.3 1.6 - - + -
400B AFH 4.2 13.5 - - - +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TRP* 3.6 13.7 - - + -
169B PHE* 3.5 23.5 - - + -
244B LEU 3.4 15.0 - - - +
245B GLU 3.2 6.7 + - - +
246B GLY 3.1 0.6 - - - -
247B VAL* 1.3 81.2 - - - +
249B ARG* 1.3 59.6 + - - +
251B LEU* 3.3 3.0 + - - -
252B ALA* 2.8 30.8 + - - +
267B LEU* 4.0 18.2 - - + -
271B LEU* 3.5 6.3 - - + +
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B HIS* 5.5 0.8 + - - -
169B PHE* 3.8 19.5 - - + -
172B ASN* 2.6 52.9 + - - +
173B LEU* 4.9 0.7 - - - -
174B PRO* 3.6 21.9 - - + +
245B GLU* 3.1 39.6 + - - +
246B GLY* 3.2 15.7 + - - +
248B ALA* 1.3 77.3 - - - +
250B VAL* 1.3 64.6 + - + +
252B ALA* 3.3 6.0 + - - +
253B GLY 3.2 15.6 + - - -
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B PRO* 4.9 3.8 - - + -
180B TYR* 2.8 35.7 + - + +
182B VAL* 3.8 22.4 - - + -
214B LYS* 4.3 11.7 - - + +
239B LEU* 4.1 22.9 - - + -
242B MET* 3.5 32.3 - - + -
246B GLY 3.3 5.3 + - - +
247B VAL* 3.6 8.1 - - + +
248B ALA 3.2 0.2 - - - -
249B ARG* 1.3 78.1 - - + +
251B LEU* 1.3 63.7 + - + +
253B GLY 3.0 4.3 + - - -
254B ALA 3.2 4.3 + - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B VAL* 3.9 21.3 - - + -
184B LEU* 4.3 7.2 - - + -
247B VAL* 3.0 23.9 + - + +
248B ALA 3.6 4.0 - - - +
250B VAL* 1.3 75.8 - - + +
252B ALA* 1.3 63.9 + - - +
254B ALA* 3.0 18.5 + - - +
257B VAL* 3.9 18.4 - - + -
264B LEU* 3.7 26.2 - - + +
267B LEU* 3.7 32.8 - - + -
268B THR* 3.4 21.5 - - - +
271B LEU* 3.7 9.0 - - + -
273B ARG* 3.3 17.0 - - - +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ALA* 5.8 2.7 - - + +
169B PHE* 4.0 18.6 - - + -
173B LEU* 3.9 23.8 - - + +
248B ALA 2.8 21.0 + - - +
249B ARG 3.4 6.3 - - - +
250B VAL 3.2 0.2 - - - -
251B LEU* 1.3 73.1 - - - +
253B GLY* 1.3 55.7 + - - +
271B LEU* 3.9 16.3 - - + +
273B ARG* 3.3 26.1 + - - +
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU* 4.5 2.7 - - - +
174B PRO* 3.9 14.8 - - - -
177B ALA* 3.3 10.2 - - - -
178B GLY 2.8 28.0 + - - -
180B TYR* 3.2 22.6 - - - -
249B ARG 3.2 5.9 + - - -
250B VAL 3.0 4.6 + - - -
252B ALA* 1.3 76.5 - - - +
254B ALA* 1.3 60.1 + - - +
273B ARG* 4.7 2.0 - - - -
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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