Contacts of the helix formed by residues 296 - 313 (chain A) in PDB entry 2H0A
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 PRO 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 4.8 0.4 - - - +
160A LEU* 3.6 17.9 - - + -
294A ALA 4.1 2.2 - - - +
295A GLN* 1.3 79.7 - - + +
297A VAL* 1.3 58.0 + - - +
298A GLU* 3.4 5.4 - - - +
299A ALA* 3.3 16.5 + - + -
300A MET* 2.9 30.7 + - + +
324A PHE* 3.5 30.5 - - + -
325A GLU 4.0 14.4 - - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.3 54.7 - - + +
80A ARG* 3.6 29.6 - - + +
81A LEU* 3.4 27.0 - - + +
295A GLN* 3.0 19.5 + - + +
296A PRO* 1.3 68.7 - - - +
298A GLU* 1.3 71.3 + - - +
300A MET* 3.2 10.3 + - - +
301A GLY* 3.0 17.5 + - - -
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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
----------------------------------------------------------
79A ARG* 5.6 0.9 + - - -
80A ARG* 3.1 67.3 + - + +
83A GLU* 4.5 17.3 - - + +
84A GLY* 3.3 16.5 - - - +
283A PRO* 5.1 5.4 - - - +
296A PRO* 4.1 1.9 - - - +
297A VAL* 1.3 71.2 + - - +
299A ALA* 1.3 52.5 + - - +
301A GLY 2.9 3.5 + - - -
302A ALA* 2.7 34.6 + - - +
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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
----------------------------------------------------------
296A PRO* 3.3 18.2 + - + +
298A GLU* 1.3 79.0 - - - +
300A MET* 1.3 57.5 + - - +
302A ALA* 3.7 8.7 - - - +
303A ARG* 2.8 31.7 + - - +
324A PHE* 3.6 19.5 - - + -
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Residues in contact with MET 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 5.1 4.5 - - + -
81A LEU* 4.4 2.0 - - + -
148A VAL* 3.6 6.7 - - + +
149A ASP* 4.3 26.0 - - + +
158A VAL* 3.4 15.6 - - + +
159A TYR* 4.0 11.0 - - - -
160A LEU* 3.9 46.4 - - + +
295A GLN* 4.4 9.0 - - - +
296A PRO* 2.9 25.4 + - - +
297A VAL* 3.4 18.2 - - - +
299A ALA* 1.3 78.0 - - - +
301A GLY* 1.3 57.0 + - - +
303A ARG* 3.8 0.2 - - - +
304A ALA* 3.0 27.0 + - - +
324A PHE* 3.8 27.1 - - + -
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.6 27.3 - - - +
84A GLY 3.9 0.7 - - - -
85A ILE* 3.4 17.9 - - - +
148A VAL* 4.6 0.7 - - - -
297A VAL 3.0 7.8 + - - -
298A GLU 2.9 6.0 + - - -
300A MET* 1.3 75.2 - - - +
302A ALA* 1.3 59.6 + - - +
304A ALA* 3.0 8.0 + - - +
305A ALA* 2.8 25.6 + - - +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY* 3.2 17.4 + - - +
88A VAL* 3.4 26.1 - - + +
298A GLU 2.7 18.6 + - - +
299A ALA* 3.7 9.4 - - - +
301A GLY* 1.3 71.9 - - - +
303A ARG* 1.3 61.7 + - - +
305A ALA* 3.2 3.4 + - - +
306A GLN* 3.0 22.2 + - - +
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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
----------------------------------------------------------
158A VAL* 4.5 3.1 - - + -
299A ALA 2.8 22.1 + - - +
300A MET 3.8 3.4 - - - +
302A ALA* 1.3 73.5 - - - +
304A ALA* 1.3 62.7 - - - +
306A GLN* 3.3 25.0 + - - +
307A LEU* 3.1 39.3 + - + +
310A GLU* 4.8 4.0 + - - -
322A VAL* 3.9 37.3 - - + +
324A PHE* 3.7 14.9 - - + -
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 4.4 15.0 - - + -
146A VAL* 3.5 22.8 - - + +
148A VAL* 3.7 18.6 - - + -
158A VAL* 3.6 21.1 - - + +
300A MET 3.0 16.1 + - - +
301A GLY* 3.2 11.0 - - - +
303A ARG* 1.3 78.1 - - - +
305A ALA* 1.3 61.5 + - - +
307A LEU* 4.6 0.2 - - - -
308A LEU 3.3 15.1 + - - -
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.1 11.2 - - + +
88A VAL* 3.6 26.0 - - + -
89A LEU* 3.9 19.3 - - + +
124A ILE* 4.2 10.5 - - - +
301A GLY 2.8 12.5 + - - +
302A ALA 3.4 7.9 - - - +
303A ARG 3.2 0.2 - - - -
304A ALA* 1.3 73.9 - - - +
306A GLN* 1.3 65.2 + - - +
308A LEU* 3.0 5.9 + - - +
309A LEU* 2.9 24.6 + - - +
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 4.1 10.8 - - + +
92A GLN* 5.9 0.8 - - - +
302A ALA 3.0 13.1 + - - +
303A ARG* 3.7 28.7 - - - +
305A ALA* 1.3 75.9 - - - +
307A LEU* 1.3 63.8 + - - +
309A LEU* 3.1 22.9 + - - +
310A GLU* 2.9 52.3 + - - +
313A ARG* 5.6 3.2 + - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 4.1 15.3 - - + -
156A ASP* 4.2 10.8 - - + +
157A SER 4.9 4.5 - - - +
158A VAL* 4.0 23.1 - - + -
303A ARG* 3.1 39.2 + - + +
304A ALA 3.9 2.7 - - - +
306A GLN* 1.3 75.3 - - - +
308A LEU* 1.3 63.3 + - - +
310A GLU* 3.2 8.0 + - - +
311A ARG* 3.0 20.5 + - - +
320A ARG* 3.1 57.0 + - + +
321A GLU 5.9 0.2 - - - -
322A VAL* 4.6 14.6 - - + +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.1 30.3 - - - +
89A LEU* 4.9 3.4 - - + -
122A GLY* 4.1 9.2 - - - -
123A LEU 3.8 5.8 - - - +
124A ILE* 3.4 22.2 - - + -
144A PRO* 3.7 29.8 - - + +
145A VAL 4.8 0.2 - - - +
146A VAL* 3.5 21.5 - - + +
304A ALA 3.3 11.1 + - - +
305A ALA 3.0 10.5 + - - +
307A LEU* 1.3 79.7 - - - +
309A LEU* 1.3 50.0 + - - +
311A ARG* 3.1 6.9 + - + +
312A MET* 2.6 54.4 + - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 4.4 13.2 - - + -
89A LEU* 4.1 10.3 - - + -
92A GLN* 3.3 31.2 - - + -
94A TYR* 3.6 36.1 - - + +
305A ALA 2.9 11.9 + - - +
306A GLN* 3.4 27.1 - - - +
308A LEU* 1.3 71.7 - - - +
310A GLU* 1.3 57.8 + - - +
312A MET* 3.4 14.7 - - + -
313A ARG* 2.6 62.6 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ARG* 4.8 3.8 + - - -
306A GLN* 2.9 47.9 + - - +
307A LEU* 3.4 11.4 - - - +
309A LEU* 1.3 76.5 - - - +
311A ARG* 1.3 60.3 + - - +
313A ARG* 3.3 11.8 + - - +
315A TYR* 2.9 33.6 + - + +
320A ARG* 2.4 40.0 + - - +
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 4.1 25.9 - - + +
156A ASP* 2.4 55.3 + - - +
307A LEU 3.0 9.2 + - - +
308A LEU* 3.4 10.3 - - + +
310A GLU* 1.3 73.8 - - - +
312A MET* 1.3 65.0 + - - +
313A ARG 3.0 1.3 - - - -
314A GLY* 3.2 12.1 + - - -
315A TYR* 3.5 32.7 + - - +
316A GLN* 4.4 0.6 - - - +
317A GLY 2.2 47.9 + - - +
318A PRO 3.7 7.1 + - - -
319A PRO* 4.2 3.2 - - - +
320A ARG* 3.6 13.7 - - - +
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 4.9 2.9 - - - -
89A LEU* 4.7 4.0 - - + -
94A TYR* 3.2 44.6 + - + +
121A ASP* 3.6 18.2 - - + +
122A GLY* 3.5 28.7 - - - -
144A PRO* 3.7 22.9 - - + -
308A LEU* 2.6 38.5 + - + +
309A LEU* 3.0 20.4 + - + +
311A ARG* 1.3 72.7 - - - +
313A ARG* 1.3 58.8 + - + +
314A GLY 3.2 3.6 + - - -
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 2.6 42.4 + - - +
94A TYR* 4.7 14.1 + - - +
306A GLN* 5.6 3.2 + - - +
309A LEU* 2.6 51.3 + - - +
310A GLU* 3.6 6.5 - - - +
311A ARG 3.0 0.4 - - - -
312A MET* 1.3 74.1 - - - +
314A GLY* 1.3 58.9 + - - +
315A TYR 3.5 3.4 + - - -
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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
------------------------------------------------------------
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