Contacts of the helix formed by residues 295 - 310 (chain B) in PDB entry 2C1H
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 ASP 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A SER 5.1 2.0 + - - -
294B ILE* 1.3 73.0 - - - +
296B GLU* 1.3 64.8 + - - +
297B ASP* 3.0 25.6 + - - +
298B ARG* 3.1 49.2 + - + +
299B VAL* 3.1 27.8 + - + +
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.1 11.1 - - + +
286B LYS* 3.1 40.2 + - + +
289B ALA* 3.7 25.7 - - + +
294B ILE 3.7 4.6 + - - -
295B ASP* 1.3 72.4 + - - +
297B ASP* 1.3 76.5 + - - +
299B VAL* 4.0 0.2 - - - -
300B MET* 3.0 43.8 + - + +
319B TYR* 4.0 16.9 + - - -
322B GLU* 5.4 2.3 - - - +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP* 3.0 10.1 + - - +
296B GLU* 1.3 86.8 + - - +
298B ARG* 1.3 64.3 + - + +
300B MET* 4.0 1.2 - - - +
301B MET* 3.1 32.4 + - - +
319B TYR* 3.6 13.8 + - - -
322B GLU* 5.8 0.2 - - - +
326B LYS* 2.7 35.5 + - + +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER 5.4 0.8 + - - -
204A SER* 3.4 38.7 + - - +
210A ARG* 5.8 3.6 - - - +
295B ASP* 3.1 41.7 + - - +
297B ASP* 1.3 77.4 - - + +
299B VAL* 1.3 59.6 + - - +
301B MET* 3.6 4.2 + - - +
302B GLU* 3.0 30.7 + - - +
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Residues in contact with VAL 299 (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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204A SER* 3.5 33.9 - - - +
205A PHE* 3.7 28.2 - - + -
284A MET* 4.4 8.5 - - + -
256B LEU* 6.4 0.2 - - + -
285B VAL* 3.9 30.1 - - + -
294B ILE* 4.1 18.2 - - + -
295B ASP 3.1 18.8 + - - +
296B GLU 4.1 1.6 - - - +
298B ARG* 1.3 72.8 - - - +
300B MET* 1.3 55.7 + - - +
302B GLU* 3.3 1.0 + - - +
303B SER* 2.6 38.7 + - - +
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Residues in contact with MET 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B HIS* 4.3 17.4 + - - -
282B TYR* 3.9 30.1 - - + +
285B VAL* 3.7 32.3 - - + -
286B LYS* 4.2 14.6 - - + -
296B GLU* 3.0 26.2 + - + +
297B ASP 4.0 0.2 - - - +
299B VAL* 1.3 75.8 - - - +
301B MET* 1.3 57.8 + - - +
303B SER* 2.9 16.5 + - - -
304B LEU* 3.1 25.0 + - - +
319B TYR* 3.5 59.0 - - + -
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Residues in contact with MET 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.6 29.9 - - + +
297B ASP 3.1 22.4 + - - +
298B ARG* 4.0 4.5 - - - +
300B MET* 1.3 74.4 - - - +
302B GLU* 1.3 61.8 + - - +
304B LEU* 3.3 6.7 + - - +
305B LEU* 3.0 27.4 + - - +
319B TYR* 4.5 4.7 - - + -
323B ALA* 4.1 30.1 - - - +
326B LYS* 4.1 24.5 - - + -
327B LEU* 4.3 21.1 - - + -
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ALA 4.4 1.0 - - - +
203A SER* 2.5 29.8 + - - -
204A SER* 2.6 38.5 + - - +
205A PHE* 3.3 14.2 - - + -
229A PRO* 4.1 16.2 - - + -
258A TYR* 2.9 26.3 + - - +
298B ARG 3.0 16.8 + - - +
299B VAL 3.8 2.7 - - - +
301B MET* 1.3 76.0 - - - +
303B SER* 1.3 58.4 + - - +
305B LEU* 3.1 9.3 + - + +
306B CYS* 2.8 34.5 + - - -
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 4.5 9.6 - - - -
257A ALA* 5.0 0.2 - - - -
256B LEU* 3.4 35.4 - - - +
277B HIS* 4.4 11.8 + - - -
285B VAL* 5.4 2.0 - - - +
299B VAL* 2.6 26.2 + - - +
300B MET* 2.9 17.7 + - - -
302B GLU* 1.3 75.3 - - - +
304B LEU* 1.3 59.5 + - - +
306B CYS* 3.5 9.9 + - - +
307B MET* 3.3 29.2 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.3 33.1 - - + +
36B LEU* 4.2 10.1 - - + -
277B HIS* 4.1 12.8 - - + +
300B MET 3.1 21.9 + - - +
301B MET* 3.6 10.1 - - - +
303B SER* 1.3 74.1 - - - +
305B LEU* 1.3 63.1 + - - +
307B MET* 3.5 10.6 + - - +
308B LYS* 3.3 16.3 + - - +
315B ILE* 3.9 28.6 - - + +
317B THR* 4.0 20.2 - - + +
319B TYR* 4.5 8.1 - - + -
323B ALA* 3.8 28.9 - - + -
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Residues in contact with LEU 305 (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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228A ASN* 4.6 4.0 - - - +
229A PRO* 4.3 14.4 - - + +
230A ALA* 3.5 41.7 - - + +
27B GLN* 5.0 5.2 - - - +
29B ASN* 3.8 18.4 - - + +
30B THR* 4.4 8.1 - - - +
31B LEU* 4.3 15.5 - - + +
301B MET 3.0 14.1 + - - +
302B GLU* 3.1 11.4 + - - +
304B LEU* 1.3 73.9 - - - +
306B CYS* 1.3 60.4 + - - +
308B LYS* 3.1 5.7 + - + -
309B ARG* 2.9 27.5 + - - +
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Residues in contact with CYS 306 (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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205A PHE* 5.9 0.4 - - - -
229A PRO 4.5 1.6 - - - -
257A ALA* 3.3 33.9 - - + +
258A TYR* 3.4 26.0 - - - -
259B LEU* 4.0 9.6 - - + +
302B GLU* 2.8 24.6 + - - -
303B SER* 3.5 12.1 - - - +
305B LEU* 1.3 76.6 - - - +
307B MET* 1.3 55.8 + - - +
309B ARG* 3.4 27.1 + - - +
310B ALA* 2.9 28.1 + - - +
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Residues in contact with MET 307 (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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255B GLY* 4.0 9.2 - - - -
256B LEU* 3.6 33.9 - - + +
259B LEU* 4.0 12.3 - - + -
262B VAL* 4.7 0.2 - - - +
275B ILE* 3.8 22.4 - - + -
277B HIS* 3.5 34.1 - - + +
303B SER 3.3 13.8 + - - +
304B LEU* 3.6 15.5 - - - +
305B LEU 3.2 0.6 - - - -
306B CYS* 1.3 74.5 - - - +
308B LYS* 1.3 63.6 + - - +
310B ALA* 3.4 8.3 + - - +
311B GLY 3.5 0.5 + - - -
312B ALA* 3.2 25.1 + - - +
315B ILE* 3.9 34.5 - - + -
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Residues in contact with LYS 308 (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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29B ASN* 4.1 17.6 - - + +
30B THR 2.8 33.1 + - - +
31B LEU* 3.8 26.0 - - + -
32B THR* 4.8 2.0 + - - +
35B ASP* 2.9 38.8 + - + +
304B LEU 3.3 1.9 + - - +
305B LEU* 3.1 15.3 + - + +
307B MET* 1.3 74.7 - - - +
309B ARG* 1.3 64.7 + - - +
311B GLY* 3.1 14.7 + - - -
312B ALA 3.2 24.9 + - - +
313B ASP* 5.0 5.8 - - - +
315B ILE* 4.0 8.1 - - + -
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Residues in contact with ARG 309 (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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201A TYR* 4.5 0.7 - - - -
229A PRO 2.5 34.7 + - - -
230A ALA 3.2 16.6 - - - +
231A ASN 3.2 26.9 - - - -
232A THR* 3.0 28.0 + - - +
257A ALA 3.2 21.6 + - - -
258A TYR* 3.3 22.6 - - - +
260A ASP* 2.9 34.5 + - - +
261A ILE* 3.4 8.7 - - - +
29B ASN* 3.4 13.1 + - + +
259B LEU* 5.0 0.2 - - - +
263B TRP* 4.1 9.0 - - - -
305B LEU 2.9 11.9 + - - +
306B CYS* 3.4 35.4 + - - +
307B MET 3.3 0.2 - - - -
308B LYS* 1.3 73.1 - - - +
310B ALA* 1.3 56.2 + - - +
311B GLY* 2.9 11.2 + - - -
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Residues in contact with ALA 310 (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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260A ASP* 3.3 15.4 + - - +
259B LEU* 3.4 49.8 - - + +
262B VAL* 3.7 5.9 - - + +
263B TRP* 3.3 33.5 + - - -
306B CYS 2.9 9.8 + - - +
307B MET 3.7 6.5 - - - +
308B LYS 3.3 0.6 - - - -
309B ARG* 1.3 75.1 - - - +
311B GLY* 1.3 57.9 + - - +
312B ALA 3.7 0.4 - - - -
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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
------------------------------------------------------------
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