Contacts of the helix formed by residues 292 - 306 (chain A) in PDB entry 2H07
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 ILE 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.4 3.6 - - + -
127A MET* 3.8 24.5 - - + -
147A ALA* 4.8 5.8 - - + -
150A ALA* 5.4 1.3 - - + -
272A THR* 4.0 15.3 - - + -
273A ASN* 3.7 18.1 - - + +
274A THR* 3.9 36.6 - - + +
290A ILE* 4.3 9.4 - - + +
291A ASP* 1.3 75.6 + - - +
293A SER* 1.3 66.4 + - - +
294A MET* 3.2 8.5 - - - -
295A ILE* 3.0 27.8 + - + +
296A LEU* 3.1 35.1 + - + +
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Residues in contact with SER 293 (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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15A LEU* 3.8 22.0 - - - -
18A LYS* 3.7 29.2 - - - +
19A ILE* 3.9 5.9 - - - +
22A ARG* 3.1 13.0 + - - -
291A ASP* 2.8 32.8 + - - -
292A ILE* 1.3 79.8 - - - +
294A MET* 1.3 58.7 + - - +
296A LEU* 3.3 2.6 + - - +
297A ALA* 2.8 31.5 + - - +
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Residues in contact with MET 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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22A ARG* 3.3 40.8 - - - +
150A ALA* 6.0 3.8 - - + -
290A ILE* 6.3 0.2 - - + -
291A ASP* 2.9 30.5 - - - +
292A ILE* 3.5 5.8 - - - -
293A SER* 1.3 76.4 + - - +
295A ILE* 1.3 87.6 + - + +
297A ALA* 3.8 1.0 - - - +
298A GLU* 3.0 31.2 + - - +
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Residues in contact with ILE 295 (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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127A MET* 3.9 10.1 - - + -
145A LEU* 3.8 29.6 - - + -
146A TYR 4.3 17.0 - - - +
147A ALA* 5.2 0.2 - - - -
149A PRO* 6.3 1.1 - - + -
150A ALA* 5.0 12.1 - - + +
292A ILE* 3.0 28.2 + - + +
294A MET* 1.3 103.0 - - + +
296A LEU* 1.3 61.7 + - - +
298A GLU* 3.4 4.0 + - - -
299A ALA* 3.1 19.2 + - - +
312A LEU* 3.5 23.7 - - + +
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Residues in contact with LEU 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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15A LEU* 3.9 26.9 - - + -
19A ILE* 3.8 15.5 - - + -
88A VAL* 4.6 11.4 - - + -
90A PRO* 3.9 16.4 - - + -
125A ILE* 4.4 12.3 - - + +
126A THR 5.3 1.8 - - - +
127A MET* 4.4 15.0 - - + -
145A LEU* 3.6 26.5 - - + -
292A ILE* 3.1 33.9 + - + +
293A SER 3.7 5.4 - - - +
295A ILE* 1.3 73.1 - - - +
297A ALA* 1.3 64.3 + - - +
299A ALA* 3.2 3.3 + - - +
300A ILE* 3.1 28.5 + - - +
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Residues in contact with ALA 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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19A ILE* 4.0 25.0 - - + +
22A ARG* 3.8 29.4 - - + -
23A LEU* 3.6 12.5 - - + +
293A SER 2.8 17.3 + - - +
294A MET 3.8 3.8 - - - +
296A LEU* 1.3 75.5 - - - +
298A GLU* 1.3 58.6 + - - +
300A ILE* 3.3 3.7 + - - +
301A ARG* 3.0 29.6 + - - +
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Residues in contact with GLU 298 (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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294A MET 3.0 19.4 + - - +
295A ILE* 3.6 5.4 - - - +
297A ALA* 1.3 76.0 - - - +
299A ALA* 1.3 58.6 + - - +
301A ARG* 2.5 32.6 + - - -
302A ARG* 2.5 63.5 + - - +
311A TYR* 6.0 0.4 - - + -
312A LEU* 3.3 31.0 - - + -
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Residues in contact with ALA 299 (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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125A ILE* 4.3 14.8 - - + -
143A ASP* 6.1 0.7 - - + -
145A LEU* 4.0 18.4 - - + -
295A ILE 3.1 16.5 + - - +
296A LEU 3.2 5.6 + - - +
298A GLU* 1.3 73.3 - - - +
300A ILE* 1.3 57.6 + - - +
302A ARG* 3.7 1.8 - - - +
303A THR* 2.7 39.6 + - - +
309A VAL* 4.0 17.1 - - + +
312A LEU* 3.6 13.6 - - + +
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Residues in contact with ILE 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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4A ILE* 3.9 17.7 - - + -
6A ILE* 4.6 4.5 - - + -
19A ILE* 3.8 30.1 - - + -
23A LEU* 4.0 7.6 - - + -
54A TYR* 3.5 47.0 + - + -
56A VAL* 5.0 3.6 - - + -
88A VAL* 4.0 23.1 - - + -
125A ILE* 4.1 11.2 - - + -
296A LEU 3.1 13.4 + - - +
297A ALA 3.3 6.5 + - - +
299A ALA* 1.3 74.2 - - - +
301A ARG* 1.3 61.2 + - - +
303A THR* 3.1 3.2 + - - -
304A HIS* 2.8 29.1 + - - +
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Residues in contact with ARG 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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4A ILE* 5.5 2.2 - - - -
23A LEU* 3.6 22.2 - - + +
297A ALA 3.0 16.8 + - - +
298A GLU* 2.5 42.8 + - - +
300A ILE* 1.3 78.0 - - - +
302A ARG* 1.3 72.8 + - - +
304A HIS* 3.3 5.5 + - - +
305A ASN* 2.8 54.8 + - - +
307A GLU* 6.1 2.8 - - - +
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Residues in contact with ARG 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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298A GLU* 2.5 55.7 + - - +
299A ALA 3.9 0.2 - - - +
301A ARG* 1.3 86.6 - - - +
303A THR* 1.3 60.3 + - - +
305A ASN* 4.8 0.9 - - - -
306A GLY* 3.0 7.6 + - - -
307A GLU* 2.8 79.1 + - + +
308A SER* 2.5 32.8 + - - -
309A VAL* 3.9 11.2 - - + +
311A TYR* 3.1 39.2 - - - +
312A LEU* 4.0 11.1 - - - +
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Residues in contact with THR 303 (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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54A TYR* 3.4 20.4 - - + +
84A ARG* 3.3 21.8 + - - +
86A THR* 4.8 0.2 - - - +
123A HIS* 3.6 37.2 + - + +
125A ILE* 3.9 5.8 - - - +
143A ASP* 4.2 1.7 + - - -
299A ALA* 2.7 28.1 + - - +
300A ILE* 3.5 7.4 - - - -
302A ARG* 1.3 73.5 - - - +
304A HIS* 1.3 61.0 + - - +
306A GLY* 3.5 9.8 + - - -
309A VAL* 3.9 12.8 - - - +
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Residues in contact with HIS 304 (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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3A ASN* 2.8 36.0 + - - +
4A ILE* 4.1 31.0 - - + +
52A ASP* 2.5 37.6 + - + +
54A TYR* 3.5 7.9 - - + +
84A ARG* 4.0 2.6 + - - +
300A ILE 2.8 16.2 + - - +
301A ARG* 3.5 6.7 - - - +
303A THR* 1.3 78.8 - - - +
305A ASN* 1.3 74.8 + - - +
306A GLY 3.2 1.4 + - - -
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Residues in contact with ASN 305 (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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301A ARG* 2.8 54.6 + - - +
302A ARG* 4.8 1.3 - - - -
304A HIS* 1.3 92.5 - - - +
306A GLY* 1.3 63.1 + - - +
307A GLU* 3.3 10.1 + - + +
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Residues in contact with GLY 306 (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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302A ARG 3.0 6.7 + - - -
303A THR* 3.5 7.5 + - - -
304A HIS 3.2 5.5 + - - -
305A ASN* 1.3 77.9 - - - +
307A GLU* 1.3 61.4 + - - +
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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