Contacts of the helix formed by residues 300 - 309 (chain A) in PDB entry 3QPV
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 LEU 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A GLY 4.3 14.4 - - - +
267A ASP* 3.5 27.1 - - + +
298A SER* 2.9 8.3 + - - +
299A GLN* 1.3 85.6 - - + +
301A LYS* 1.3 66.4 + - - +
302A SER* 3.2 4.4 + - - +
303A THR* 3.2 17.3 + - - -
304A ILE* 3.5 6.4 + - - +
321A ASN* 4.0 17.9 - - + +
322A GLU* 3.7 23.8 - - + +
387A HIS* 3.5 30.1 - - + +
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Residues in contact with LYS 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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267A ASP* 2.6 32.5 + - - +
268A SER 4.3 1.6 - - - +
269A GLY* 4.0 16.4 - - - +
299A GLN 3.8 1.6 + - - -
300A LEU* 1.3 71.2 - - - +
302A SER* 1.3 54.6 + - - +
304A ILE* 3.0 10.6 + - + +
305A GLN* 2.7 62.8 + - + +
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Residues in contact with SER 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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253A HIS* 3.2 33.4 + - - +
256A ASN* 4.0 11.6 + - - -
268A SER 3.5 19.1 + - - -
269A GLY 4.6 1.8 - - - -
270A LEU* 3.7 13.4 - - - +
300A LEU* 3.2 1.8 + - - +
301A LYS* 1.3 78.4 - - - +
303A THR* 1.3 56.7 + - - +
305A GLN* 4.0 8.1 - - - -
306A THR* 2.6 33.8 + - - -
387A HIS* 4.3 7.4 - - - -
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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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253A HIS* 3.8 8.1 - - + -
297A THR* 3.3 12.7 - - - +
298A SER* 2.9 29.5 + - - +
300A LEU 3.2 5.2 + - - -
301A LYS 3.3 0.2 - - - -
302A SER* 1.3 78.2 + - - +
304A ILE* 1.3 60.4 + - - +
306A THR* 3.5 3.1 + - - -
307A ALA 3.0 21.3 + - - -
385A ILE* 3.4 28.8 - - - +
386A CYS* 3.4 19.3 - - - +
387A HIS* 3.3 31.6 - - + +
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Residues in contact with ILE 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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297A THR* 3.8 12.8 - - - +
298A SER 3.7 13.0 - - - +
299A GLN 3.8 13.9 - - - +
300A LEU 3.5 17.5 - - - +
301A LYS* 3.0 9.9 + - + +
303A THR* 1.3 76.0 - - - +
305A GLN* 1.3 67.7 + - + +
307A ALA* 3.0 4.6 + - - +
308A GLU* 2.9 25.1 + - + +
314A TYR* 3.2 28.5 - - + +
316A GLN* 3.3 35.2 - - + +
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Residues in contact with GLN 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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269A GLY* 3.1 13.5 - - - -
270A LEU* 3.0 52.3 + - + +
275A LYS* 4.8 12.3 - - - +
278A ALA* 4.7 0.3 - - - +
301A LYS* 2.7 45.0 + - + +
302A SER* 4.0 0.7 - - - -
304A ILE* 1.3 73.6 - - - +
306A THR* 1.3 63.6 + - - +
308A GLU* 3.2 21.9 + - - +
309A ALA* 3.4 6.8 + - - +
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Residues in contact with THR 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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254A GLY* 3.0 27.7 + - - +
270A LEU* 3.5 6.9 - - - +
277A PHE* 4.0 11.9 - - + -
278A ALA* 4.1 13.5 - - + +
281A LEU* 3.9 25.1 - - + -
302A SER 2.6 22.3 + - - -
303A THR 3.5 6.5 - - - -
304A ILE 3.2 0.6 - - - -
305A GLN* 1.3 77.1 - - - +
307A ALA* 1.3 61.4 + - - +
308A GLU 3.2 0.9 + - - -
309A ALA* 3.2 18.9 + - - +
310A LEU* 4.0 6.6 - - - +
385A ILE* 4.0 13.9 - - + -
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Residues in contact with ALA 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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295A VAL* 4.3 2.7 - - + -
297A THR* 3.5 31.0 - - + -
303A THR 3.0 6.4 + - - +
304A ILE 3.0 7.2 + - - +
306A THR* 1.3 76.1 - - - +
308A GLU* 1.3 61.9 + - - +
310A LEU* 3.0 23.2 + - - +
311A ARG 4.0 2.1 + - - -
312A LEU 4.7 1.9 + - - +
314A TYR* 3.8 29.9 - - + -
385A ILE* 3.9 14.1 - - + +
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Residues in contact with GLU 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 ILE* 2.9 20.7 + - + +
305A GLN* 3.4 13.5 - - + +
306A THR 3.2 0.2 - - - -
307A ALA* 1.3 76.0 - - - +
309A ALA* 1.3 63.8 + - - +
310A LEU 2.8 2.1 + - - -
311A ARG* 3.1 19.1 + - - +
314A TYR* 2.6 34.5 + - - +
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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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278A ALA* 3.2 47.3 - - + +
279A SER* 3.9 4.4 - - - +
282A SER* 3.6 14.1 + - - -
305A GLN 3.4 3.9 + - - +
306A THR 3.2 7.4 + - - +
308A GLU* 1.3 77.8 - - - +
310A LEU* 1.3 58.7 + - + +
311A ARG* 3.4 13.5 + - - +
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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
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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