Contacts of the helix formed by residues 296 - 312 (chain A) in PDB entry 2QVH
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
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Residue Dist Surf HB Arom Phob DC
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2A SER* 3.9 24.0 - - - +
5A GLY 4.2 18.2 - - - +
6A ARG* 4.7 0.7 - - - -
7A ALA* 4.0 20.6 - - + +
25A MSE 5.6 1.8 - - - -
293A GLU* 5.4 4.0 - - + +
294A ILE 3.1 6.7 - - - +
295A ASP* 1.3 89.6 - - - +
297A ALA* 1.3 56.2 + - - +
298A ALA 3.5 0.4 - - - -
299A TRP* 3.2 3.4 + - - +
300A GLN* 2.7 39.8 + - + +
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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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295A ASP* 3.2 18.2 + - - +
296A PRO* 1.3 78.9 - - - +
298A ALA* 1.3 63.7 + - - +
300A GLN* 3.2 5.8 + - - +
301A ALA* 3.0 23.6 + - - +
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Residues in contact with ALA 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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295A ASP* 4.6 4.6 + - - +
296A PRO 3.5 0.6 - - - -
297A ALA* 1.3 78.2 - - - +
299A TRP* 1.3 62.1 + - + +
301A ALA* 3.2 9.0 + - - +
302A ARG* 3.0 26.0 + - - +
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Residues in contact with TRP 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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7A ALA* 3.9 29.6 - - + -
23A GLU* 2.9 51.5 + - + +
24A GLY* 3.7 17.6 - - - +
25A MSE 4.0 10.9 - - + +
36A PHE* 3.6 43.7 - + - -
38A PRO* 3.6 15.3 - - + -
40A ALA 6.1 0.2 - - - -
294A ILE* 4.2 7.4 - - + +
295A ASP 5.0 2.6 + - - -
296A PRO 3.2 7.3 + - - +
298A ALA* 1.3 80.2 - - + +
300A GLN* 1.3 60.8 + - - +
302A ARG* 3.2 38.6 + - - +
303A LEU* 2.9 29.8 + - - +
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Residues in contact with GLN 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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5A GLY* 4.7 4.5 - - - +
25A MSE 3.0 31.2 - - - +
296A PRO* 2.7 26.8 + - + +
297A ALA* 3.6 6.1 - - - +
299A TRP* 1.3 74.2 - - - +
301A ALA* 1.3 57.1 + - - +
303A LEU* 3.3 17.0 + - - +
304A ALA* 3.0 32.8 + - + +
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Residues in contact with ALA 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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297A ALA 3.0 13.4 + - - +
298A ALA* 3.4 11.7 - - - +
300A GLN* 1.3 78.4 - - - +
302A ARG* 1.3 61.9 + - - +
304A ALA* 3.3 8.1 + - - +
305A ALA* 3.0 22.7 + - - +
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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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36A PHE* 4.2 7.2 - - + -
38A PRO* 3.1 27.1 + - - +
39A PHE 2.7 25.5 + - - -
40A ALA* 3.4 19.1 + - - +
42A TYR 3.0 26.1 + - - -
44A PRO* 5.8 3.4 - - + +
47A CYS* 3.6 16.1 - - + -
298A ALA 3.0 13.8 + - - +
299A TRP* 3.2 40.5 + - + +
301A ALA* 1.3 74.6 - - - +
303A LEU* 1.3 64.7 + - - +
305A ALA* 3.2 8.0 + - + +
306A ALA* 3.0 22.9 + - - +
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Residues in contact with LEU 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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25A MSE 3.4 30.7 - - + -
27A VAL* 3.8 16.8 - - + -
36A PHE* 3.6 32.0 - - + -
51A TRP* 3.6 37.4 - - + -
299A TRP 2.9 16.3 + - - +
300A GLN* 3.7 17.0 - - - +
301A ALA 3.3 0.2 - - - -
302A ARG* 1.3 76.1 - - - +
304A ALA* 1.3 61.5 + - - +
306A ALA* 3.3 2.4 + - - +
307A ARG* 2.9 35.3 + - + +
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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
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300A GLN* 3.0 24.2 + - - +
301A ALA* 3.5 8.3 - - - +
303A LEU* 1.3 83.8 - - - +
305A ALA* 1.3 56.4 + - - +
307A ARG* 3.4 7.7 + - - +
308A ALA* 3.0 27.7 + - - +
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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
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44A PRO* 3.9 27.4 - - + +
301A ALA 3.0 13.2 + - - +
302A ARG* 3.2 11.0 + - + +
304A ALA* 1.3 75.3 - - - +
306A ALA* 1.3 64.7 + - - +
308A ALA* 3.4 7.0 + - - +
309A ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 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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36A PHE* 3.7 12.6 - - + -
44A PRO* 3.9 12.7 - - + +
47A CYS* 3.6 37.9 - - + +
48A ALA* 3.5 6.4 - - - -
51A TRP* 3.9 4.7 - - + -
302A ARG 3.0 12.1 + - - +
303A LEU 3.7 7.6 - - - +
305A ALA* 1.3 74.3 - - - +
307A ARG* 1.3 61.7 + - - +
309A ALA* 3.3 1.0 + - - +
310A TRP* 2.9 29.6 + - - +
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Residues in contact with ARG 307 (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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51A TRP* 3.4 54.1 - - + +
55A TYR* 4.7 12.5 - - - -
303A LEU* 2.9 24.8 + - + +
304A ALA* 3.5 8.3 - - - +
306A ALA* 1.3 77.6 - - - +
308A ALA* 1.3 57.0 + - - +
310A TRP* 3.1 2.4 + - - +
311A GLU* 2.8 59.5 + - - +
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Residues in contact with ALA 308 (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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304A ALA 3.0 13.6 + - - +
305A ALA* 3.6 10.5 - - - +
307A ARG* 1.3 76.7 - - - +
309A ALA* 1.3 53.2 + - - +
311A GLU* 3.2 7.0 + - - -
312A GLN* 2.7 57.6 + - - +
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Residues in contact with ALA 309 (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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44A PRO* 3.5 32.3 - - + +
45A ARG* 4.1 12.3 - - + +
48A ALA* 4.0 8.0 - - + +
305A ALA 3.0 11.7 + - - +
306A ALA 3.6 4.7 - - - +
308A ALA* 1.3 76.8 - - - +
310A TRP* 1.3 62.6 + - - +
312A GLN* 3.6 16.4 + - - -
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Residues in contact with TRP 310 (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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48A ALA* 3.6 30.7 - - + +
49A ARG* 3.7 26.0 - - + -
51A TRP* 3.9 20.4 - + + -
52A ALA* 3.6 24.5 - - + +
55A TYR* 6.2 2.8 - + - -
208A GLY* 5.5 3.4 - - - -
306A ALA 2.9 14.3 + - - +
307A ARG 3.1 7.2 + - - +
309A ALA* 1.3 78.5 - - - +
311A GLU* 1.3 70.0 + - + +
312A GLN 3.6 2.4 + - - -
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Residues in contact with GLU 311 (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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51A TRP* 5.4 0.9 - - - +
307A ARG* 2.8 52.6 + - + +
308A ALA* 4.0 5.9 + - - +
310A TRP* 1.3 83.6 - - + +
312A GLN* 1.3 65.4 + - + +
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Residues in contact with GLN 312 (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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308A ALA* 2.7 38.5 + - - +
309A ALA* 3.7 15.3 - - - +
310A TRP 3.3 2.0 - - - -
311A GLU* 1.3 82.2 - - + +
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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