Contacts of the helix formed by residues 288 - 303 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A SER* 3.8 6.1 + - - -
260A GLY 5.1 0.2 - - - -
263A GLY* 3.3 28.9 + - - -
264A GLY 4.9 0.9 - - - -
265A VAL* 3.7 16.2 - - - -
279A SER* 2.8 21.9 + - - -
281A ARG 3.4 7.4 - - - -
282A LEU* 3.7 7.0 - - - +
287A ASN* 1.3 72.0 - - - +
289A ALA* 1.3 57.8 + - - +
291A GLY* 3.2 15.2 + - - -
292A VAL* 2.8 34.4 + - - +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 6.1 0.2 - - - +
21A PRO* 4.0 33.0 - - + +
281A ARG* 3.0 14.9 + - + +
282A LEU 4.4 0.2 - - - -
283A ASP* 4.1 25.1 - - + +
287A ASN 3.0 7.9 + - - -
288A SER* 1.3 70.4 - - - +
290A ARG* 1.3 62.4 + - + +
292A VAL* 3.6 5.4 + - - +
293A LEU* 3.2 21.5 + - - +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.0 15.3 + - + +
17A GLY* 3.9 12.1 + - - -
19A VAL 3.0 20.2 + - - +
20A ASN* 2.9 46.5 + - - +
21A PRO* 5.4 4.5 - - + -
36A PRO 4.0 4.4 + - - -
37A ASP* 4.9 8.7 + - - -
38A ARG 3.2 27.7 + - - +
39A PHE* 3.5 41.5 - - + +
279A SER* 2.8 21.7 + - - +
288A SER* 4.1 0.8 + - - -
289A ALA* 1.3 79.8 - - + +
291A GLY* 1.3 57.0 + - - +
293A LEU* 3.5 8.6 - - + +
294A ALA* 2.6 37.0 + - - +
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 4.0 10.8 - - - -
277A VAL* 3.2 28.4 - - - +
279A SER* 4.2 1.2 - - - -
288A SER* 3.2 19.5 + - - -
290A ARG* 1.3 78.0 - - - +
292A VAL* 1.3 62.7 + - - +
294A ALA* 3.3 3.3 + - - +
295A CYS* 3.2 26.3 + - - -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A MET* 4.7 6.7 - - + -
249A TRP* 3.6 31.3 - - + -
265A VAL* 4.3 6.8 - - + +
283A ASP* 4.7 9.2 - - - +
287A ASN* 4.1 25.8 - - + +
288A SER 2.8 16.9 + - - +
289A ALA 3.8 5.6 - - - +
291A GLY* 1.3 76.3 - - - +
293A LEU* 1.3 67.3 + - + +
295A CYS* 3.2 13.7 + - - +
296A ARG* 3.2 27.7 + - - +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.7 30.7 - - + -
289A ALA 3.2 14.9 + - - +
290A ARG* 3.8 7.9 - - + +
292A VAL* 1.3 81.4 - - + +
294A ALA* 1.3 65.7 + - - +
296A ARG* 3.2 25.8 + - + +
297A ARG* 3.0 29.0 + - + +
300A GLU* 6.1 0.2 - - - +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.2 5.0 - - + +
16A LEU* 3.8 17.0 - - + +
39A PHE* 4.5 6.7 - - + -
41A ILE* 4.2 16.8 - - + -
277A VAL* 4.0 17.0 - - + -
290A ARG 2.6 20.8 + - - +
291A GLY 3.4 6.3 - - - +
292A VAL 3.2 0.2 - - - -
293A LEU* 1.3 73.1 - - - +
295A CYS* 1.3 57.9 + - - +
297A ARG* 3.3 3.8 + - - +
298A LEU* 3.0 32.8 + - - +
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Residues in contact with CYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TRP* 3.8 22.2 - - + -
253A VAL* 3.6 9.7 - - + +
255A ILE* 3.6 11.2 - - + +
257A ALA* 5.1 4.0 - - - -
265A VAL* 4.1 22.0 - - - -
267A GLY* 5.9 1.3 - - - -
275A ILE* 4.7 15.0 - - - -
277A VAL* 4.2 12.6 - - - -
291A GLY 3.2 13.7 + - - -
292A VAL 3.2 9.1 + - - +
294A ALA* 1.3 77.3 - - - +
296A ARG* 1.3 65.0 + - - +
298A LEU* 3.5 6.0 + - - +
299A SER* 3.1 23.0 + - - -
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A GLN* 5.7 3.4 - - - +
249A TRP* 4.8 9.7 - - - +
252A ASP* 4.2 32.9 + - - +
253A VAL* 3.8 26.4 - - + +
292A VAL* 3.2 28.8 + - - +
293A LEU* 3.2 25.7 + - + +
295A CYS* 1.3 78.7 - - - +
297A ARG* 1.3 62.1 + - - +
299A SER* 3.4 2.4 + - - -
300A GLU* 2.9 52.9 + - - +
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 3.9 6.4 + - - -
12A LEU* 3.6 32.5 - - + +
15A GLU* 2.6 44.5 + - - -
16A LEU* 4.2 15.7 - - + +
293A LEU* 3.0 23.1 + - + +
294A ALA* 3.5 9.2 - - - +
296A ARG* 1.3 76.2 - - - +
298A LEU* 1.3 58.5 - - - +
300A GLU* 3.3 12.6 + - - -
301A ASP* 2.8 68.0 + - - -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.7 31.4 + - + -
9A LEU* 4.1 13.2 - - + -
12A LEU* 4.5 4.7 - - + -
41A ILE* 4.1 13.9 - - + -
43A LEU* 3.8 19.3 - - + -
255A ILE* 4.7 3.6 - - + -
275A ILE* 3.7 31.4 - - + -
294A ALA 3.0 20.5 + - - +
295A CYS* 3.9 9.0 - - - +
297A ARG* 1.3 75.3 - - - +
299A SER* 1.3 63.6 + - - +
302A PHE* 3.1 43.6 + - + +
304A LEU* 4.0 12.7 - - + +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP 4.4 3.5 + - - -
253A VAL* 2.6 37.4 + - - -
255A ILE* 4.0 2.9 - - - +
295A CYS 3.1 18.2 + - - -
296A ARG 3.7 4.0 - - - -
298A LEU* 1.3 78.3 - - - +
300A GLU* 1.3 55.9 + - - +
303A ARG* 2.7 35.7 + - - -
304A LEU* 3.2 20.4 + - - +
305A HIS* 3.9 10.7 - - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ASP 4.5 10.8 - - - +
293A LEU* 6.1 0.3 - - - +
296A ARG* 2.9 41.6 + - + +
297A ARG* 4.0 14.0 - - - +
299A SER* 1.3 76.3 - - - +
301A ASP* 1.3 68.4 + - - +
302A PHE 3.7 0.2 + - - -
303A ARG* 4.0 15.7 + - - +
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 2.6 38.6 + - + +
297A ARG* 2.8 52.7 + - - +
298A LEU 4.5 0.9 - - - +
300A GLU* 1.3 80.0 - - - +
302A PHE* 1.3 67.0 + - + +
303A ARG* 5.3 1.6 - - - +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.8 28.5 - - + -
8A TYR* 3.5 55.4 - + + -
43A LEU* 5.0 5.8 - - + -
298A LEU* 3.1 34.5 + - + +
301A ASP* 1.3 82.8 - - + +
303A ARG* 1.3 74.8 + - - +
304A LEU* 3.2 23.1 + - + +
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 4.5 3.3 + - - -
299A SER 2.7 15.4 + - - -
300A GLU* 4.0 15.7 - - - +
301A ASP 3.6 2.2 - - - +
302A PHE* 1.3 81.8 - - - +
304A LEU* 1.3 60.3 + - - +
305A HIS* 3.0 8.1 + - - -
308A ASP* 3.1 49.7 + - + +
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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