Contacts of the helix formed by residues 288 - 303 (chain B) in PDB entry 3IH9
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 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B SER* 3.5 7.6 + - - -
263B GLY* 3.4 23.8 + - - -
265B VAL* 3.8 17.0 - - - -
279B SER* 2.7 27.0 + - - -
281B ARG 3.3 7.0 - - - -
282B LEU* 3.5 5.2 - - - +
287B ASN* 1.3 70.2 - - - +
289B ALA* 1.3 64.2 + - - +
291B GLY* 3.1 15.3 + - - -
292B VAL* 2.9 28.4 + - - +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASN* 6.0 0.2 - - - +
21B PRO* 3.8 34.3 - - + +
281B ARG* 2.8 17.8 + - + +
283B ASP* 4.2 23.6 - - + +
287B ASN 3.0 5.2 + - - -
288B SER* 1.3 73.7 - - - +
290B ARG* 1.3 63.5 + - + +
292B VAL* 3.4 5.9 - - - +
293B LEU* 3.3 20.7 + - - +
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.2 15.0 + - + +
17B GLY* 3.8 13.5 + - - -
19B VAL* 3.2 23.2 + - + +
20B ASN* 3.2 43.3 + - - +
21B PRO* 5.2 4.5 - - + -
36B PRO 4.0 1.6 + - - -
37B ASP* 4.5 10.3 + - - -
38B ARG 2.8 30.7 + - - +
39B PHE* 3.4 41.9 - - + +
279B SER* 2.7 27.3 + - - +
288B SER* 3.4 1.0 + - - -
289B ALA* 1.3 80.2 - - + +
291B GLY* 1.3 60.5 + - - +
293B LEU* 3.7 9.9 - - + +
294B ALA* 2.8 31.5 + - - +
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Residues in contact with GLY 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B VAL* 4.1 8.9 - - - +
277B VAL* 3.6 23.6 - - - +
279B SER* 4.1 0.8 - - - -
288B SER* 3.1 25.2 + - - -
290B ARG* 1.3 80.0 - - - +
292B VAL* 1.3 61.5 + - - +
294B ALA* 3.5 3.5 + - - +
295B CYS* 3.3 25.1 + - - -
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B MET* 5.1 3.4 - - + -
249B TRP* 3.7 31.1 - - + -
259B SER* 5.3 1.3 - - - -
265B VAL* 4.9 8.7 - - + -
283B ASP* 4.2 11.4 - - - +
287B ASN* 3.5 30.1 - - + +
288B SER 2.9 19.3 + - - +
289B ALA 3.4 11.7 - - - +
291B GLY* 1.3 73.6 - - - +
293B LEU* 1.3 72.8 + - + +
295B CYS* 3.0 5.4 + - - +
296B ARG* 2.9 23.5 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.0 29.4 - - + -
19B VAL* 6.5 0.9 - - + -
289B ALA 3.3 13.8 + - - +
290B ARG* 3.8 9.0 - - + +
292B VAL* 1.3 85.8 - - + +
294B ALA* 1.3 55.7 + - - +
296B ARG* 3.4 25.2 + - + +
297B ARG* 3.0 32.5 + - + +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.3 4.1 - - + +
16B LEU* 3.7 16.6 - - + +
39B PHE* 4.4 6.3 - - + -
41B ILE* 4.4 15.3 - - + -
277B VAL* 4.2 16.2 - - + -
290B ARG 2.8 19.0 + - - +
291B GLY 3.6 6.1 - - - +
292B VAL 3.1 0.2 - - - -
293B LEU* 1.3 73.8 - - - +
295B CYS* 1.3 60.7 + - - +
297B ARG* 3.3 4.7 + - - +
298B LEU* 2.9 34.1 + - - +
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Residues in contact with CYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TRP* 3.6 25.8 - - + -
253B VAL* 3.7 6.5 - - + +
255B ILE* 3.7 8.6 - - + +
257B ALA* 5.1 4.9 - - - -
265B VAL* 4.2 20.9 - - - -
267B GLY* 5.9 1.3 - - - -
275B ILE* 4.7 14.6 - - - -
277B VAL* 4.5 11.4 - - - -
291B GLY 3.3 15.0 + - - -
292B VAL 3.0 8.4 + - - +
294B ALA* 1.3 74.6 - - - +
296B ARG* 1.3 67.8 + - - +
298B LEU* 3.3 9.4 + - - +
299B SER* 3.0 24.4 + - - -
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLN* 4.1 7.1 - - - +
249B TRP* 5.7 0.4 - - + -
252B ASP* 3.2 41.5 + - - +
253B VAL* 3.9 22.7 - - + +
292B VAL 2.9 12.1 + - - +
293B LEU* 3.6 27.6 - - + +
295B CYS* 1.3 77.9 - - - +
297B ARG* 1.3 55.9 + - + +
299B SER* 3.7 1.7 - - - -
300B GLU* 2.9 58.1 + - + +
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.9 7.6 + - - -
12B LEU* 3.8 32.6 - - + +
15B GLU* 2.9 43.2 + - - -
16B LEU* 4.3 12.6 - - + +
293B LEU* 3.0 23.2 + - + +
294B ALA 3.6 7.6 - - - +
295B CYS 3.1 0.2 - - - -
296B ARG* 1.3 73.7 - - - +
298B LEU* 1.3 60.5 + - - +
300B GLU* 3.2 15.1 + - - -
301B ASP* 2.8 70.7 + - - +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.5 31.2 - - + -
9B LEU* 3.9 14.1 - - + -
12B LEU* 4.2 3.4 - - + -
41B ILE* 3.8 20.6 - - + -
43B LEU* 3.8 14.8 - - + -
255B ILE* 4.9 1.8 - - + -
275B ILE* 3.6 32.5 - - + -
277B VAL* 5.8 0.2 - - + -
294B ALA 2.9 18.5 + - - +
295B CYS* 3.7 7.9 - - - +
297B ARG* 1.3 76.0 - - - +
299B SER* 1.3 63.6 + - - +
302B PHE* 3.1 41.0 + - + +
304B LEU* 4.0 12.4 - - + +
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP 4.2 3.6 + - - -
253B VAL* 2.4 38.8 + - - -
255B ILE* 3.8 4.9 - - - +
295B CYS 3.0 16.9 + - - -
296B ARG 3.7 4.5 - - - -
298B LEU* 1.3 77.7 - - - +
300B GLU* 1.3 56.0 + - - +
303B ARG* 2.9 31.2 + - - -
304B LEU* 2.8 21.0 + - - -
305B HIS* 3.9 7.6 - - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP 4.8 10.6 - - - +
296B ARG* 2.9 40.7 + - + +
297B ARG* 4.0 18.0 - - - +
299B SER* 1.3 78.9 - - - +
301B ASP* 1.3 67.2 + - - +
302B PHE 3.6 0.2 + - - -
303B ARG* 3.9 12.6 + - - +
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Residues in contact with ASP 301 (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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8B TYR* 2.5 38.1 + - + +
297B ARG* 2.8 56.5 + - - +
298B LEU 4.6 0.2 - - - +
300B GLU* 1.3 79.2 - - - +
302B PHE* 1.3 65.4 + - + +
303B ARG* 5.7 0.7 - - - +
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Residues in contact with PHE 302 (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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5B ILE* 4.8 24.0 - - + -
8B TYR* 3.6 54.3 - + + -
43B LEU* 5.1 4.0 - - + -
298B LEU* 3.1 30.8 + - + +
301B ASP* 1.3 82.3 - - - +
303B ARG* 1.3 71.3 + - - +
304B LEU* 3.3 26.0 + - + +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 3.5 9.9 + - - -
299B SER 2.9 13.6 + - - -
300B GLU* 3.9 9.3 + - - +
301B ASP 3.6 1.6 - - - +
302B PHE* 1.3 79.2 - - - +
304B LEU* 1.3 59.8 + - - +
305B HIS* 3.0 10.3 + - - -
308B ASP* 2.9 47.5 + - + +
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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