Contacts of the helix formed by residues 309 - 319 (chain A) in PDB entry 6MOL
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 HIS 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A ALA 3.7 20.0 - - - -
277A ARG 4.0 5.8 + - - -
278A ALA 4.3 2.6 - - - -
279A GLY* 3.5 26.7 + - - -
303A LYS 5.2 0.2 - - - -
304A ALA* 3.3 12.2 + - + +
307A ALA* 3.6 30.6 - - + +
308A GLY* 1.3 74.8 + - - +
310A LEU* 1.3 64.4 + - - +
311A GLU* 3.2 8.8 + - - +
312A ILE* 3.0 26.6 + - + +
313A VAL* 2.9 26.2 + - - +
345A ILE* 4.4 0.2 - - - -
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Residues in contact with LEU 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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308A GLY 3.0 8.8 + - - +
309A HIS* 1.3 72.2 - - - +
311A GLU* 1.3 73.9 + - + +
313A VAL* 3.4 2.0 + - + +
314A GLU* 3.0 40.6 + - + +
342A HIS* 4.0 15.5 - - + +
344A GLU* 3.7 34.1 - - + -
345A ILE* 3.7 28.5 - - + +
348A VAL* 4.0 19.1 - - + -
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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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281A LEU* 3.6 34.5 - - + -
308A GLY 5.1 0.3 - - - +
309A HIS* 3.9 7.3 + - - +
310A LEU* 1.3 91.4 + - + +
312A ILE* 1.3 62.6 + - + +
314A GLU* 3.5 11.8 + - - +
315A VAL* 3.1 27.2 + - - +
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Residues in contact with ILE 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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276A ALA* 4.0 31.9 - - + +
279A GLY* 3.6 14.6 - - - -
280A HIS 3.6 30.5 - - - +
281A LEU* 4.0 26.0 - - + +
284A VAL* 4.4 10.5 - - + -
304A ALA* 4.2 6.5 - - + -
309A HIS* 3.0 24.4 + - + +
311A GLU* 1.3 76.8 - - + +
313A VAL* 1.3 60.3 + - - +
315A VAL* 3.1 3.9 + - - +
316A LEU* 2.8 41.1 + - + +
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Residues in contact with VAL 313 (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 LEU* 3.7 22.9 - - + -
304A ALA* 3.7 10.1 - - + +
305A ALA* 3.6 33.9 - - + +
309A HIS 2.9 20.7 + - - +
310A LEU* 3.9 6.7 - - + +
312A ILE* 1.3 75.2 - - - +
314A GLU* 1.3 61.6 + - - +
316A LEU* 3.9 1.8 - - - +
317A LEU* 3.2 35.4 + - + +
345A ILE* 4.0 24.9 - - + -
348A VAL* 4.8 6.1 - - + -
349A LEU* 4.3 6.7 - - + -
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Residues in contact with GLU 314 (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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310A LEU* 3.0 41.4 + - + +
311A GLU* 3.7 9.8 - - - +
312A ILE 3.2 0.2 - - - -
313A VAL* 1.3 77.0 - - - +
315A VAL* 1.3 57.6 + - + +
317A LEU* 3.4 2.8 + - - +
318A LYS* 3.0 62.6 + - - +
348A VAL* 4.1 31.2 - - + +
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Residues in contact with VAL 315 (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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281A LEU* 3.7 18.8 - - + -
284A VAL* 4.2 7.9 - - + -
285A GLU* 3.9 28.9 - - + +
288A LEU* 3.7 22.0 - - + -
311A GLU 3.1 17.1 + - - +
312A ILE* 3.1 7.0 + - - +
314A GLU* 1.3 74.6 - - + +
316A LEU* 1.3 65.6 + - - +
318A LYS* 3.2 11.8 + - + +
319A TYR* 3.1 35.9 + - + -
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Residues in contact with LEU 316 (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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272A LEU* 4.1 25.8 - - + -
276A ALA* 4.5 2.5 - - + -
284A VAL* 4.7 3.4 - - + -
288A LEU* 4.4 8.5 - - + -
294A VAL* 3.4 26.2 - - + +
300A PRO* 4.0 16.6 - - + +
301A LEU* 3.9 46.0 - - + +
304A ALA* 4.1 4.0 - - + -
312A ILE* 2.8 36.5 + - + +
313A VAL 3.9 0.2 - - - +
315A VAL* 1.3 77.2 - - - +
317A LEU* 1.3 60.4 + - - +
319A TYR 3.3 6.8 + - - -
321A ALA* 3.1 24.9 + - + +
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Residues in contact with LEU 317 (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 LEU* 3.8 24.7 - - + -
313A VAL* 3.2 20.1 + - + +
314A GLU* 4.0 3.6 - - - +
316A LEU* 1.3 76.5 - - - +
318A LYS* 1.3 62.5 + - + +
320A GLY* 3.1 13.3 + - - -
321A ALA* 3.8 22.6 + - + +
323A VAL* 3.9 17.9 - - + -
348A VAL* 3.9 11.4 - - + -
349A LEU* 3.8 23.6 - - + -
352A ASN* 3.8 41.0 - - + +
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Residues in contact with LYS 318 (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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314A GLU* 3.0 52.1 + - - +
315A VAL* 3.2 12.5 + - + +
317A LEU* 1.3 77.1 - - + +
319A TYR* 1.3 65.5 + - + +
320A GLY 3.4 0.6 + - - -
352A ASN* 5.9 1.6 - - - +
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Residues in contact with TYR 319 (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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285A GLU* 4.1 5.0 + - + +
288A LEU* 3.5 62.1 - - + -
289A LYS* 3.2 32.5 - - - +
294A VAL* 3.7 12.3 - - + +
315A VAL* 3.1 37.9 + - + +
316A LEU 3.3 4.2 + - - +
317A LEU 3.2 0.6 - - - -
318A LYS* 1.3 82.1 - - + +
320A GLY* 1.3 58.8 + - - +
321A ALA 3.8 0.7 - - - -
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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