Contacts of the helix formed by residues 302 - 316 (chain A) in PDB entry 3V6A
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 LYS 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A THR* 4.5 11.6 + - + -
264A GLU* 3.0 33.0 - - - +
300A MET* 3.5 3.4 - - + +
301A GLU* 1.3 83.6 - - + +
303A LEU* 1.3 63.8 + - - +
304A GLU 3.6 1.3 - - - -
305A THR* 3.2 17.7 - - + +
306A ASN* 2.8 36.3 + - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A MET* 3.7 44.8 + - + +
301A GLU 2.8 10.9 + - - +
302A LYS* 1.3 70.7 - - - +
304A GLU* 1.3 56.0 + - - +
306A ASN* 3.0 4.1 + - - +
307A LEU* 2.8 43.0 + - + +
353A LEU* 4.8 16.6 - - + +
356A LYS* 4.3 23.6 - - + +
357A LEU* 4.1 31.9 - - + +
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Residues in contact with GLU 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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302A LYS 3.6 0.4 - - - -
303A LEU* 1.3 78.9 - - - +
305A THR* 1.3 59.7 + - - +
307A LEU* 3.4 3.6 + - - +
308A ARG* 2.8 33.5 + - + +
357A LEU* 4.3 22.5 - - + +
360A PHE* 4.1 24.1 - - + -
363A ALA* 5.6 5.4 - - - +
364A LYS* 5.8 3.6 - - - +
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Residues in contact with THR 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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264A GLU* 4.8 2.2 + - - +
302A LYS* 3.2 42.0 - - + +
304A GLU* 1.3 79.0 - - - +
306A ASN* 1.3 59.9 - - - +
308A ARG* 3.4 12.8 - - - +
309A LYS* 2.8 44.9 + - - +
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Residues in contact with ASN 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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260A THR* 3.3 17.8 + - - +
263A CYS* 3.3 34.7 - - + +
264A GLU* 3.4 18.4 - - - +
300A MET* 3.0 32.8 - - + +
302A LYS* 2.8 38.2 + - - +
303A LEU 3.3 3.4 - - - +
305A THR* 1.3 75.3 - - - +
307A LEU* 1.3 62.8 + - - +
308A ARG 2.9 4.9 + - - -
309A LYS* 3.1 17.4 + - - +
310A LEU* 3.3 11.8 + - - +
353A LEU* 5.8 0.7 - - + -
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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
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303A LEU* 2.8 24.0 + - + +
304A GLU 3.8 3.8 - - - +
306A ASN* 1.3 71.2 - - - +
308A ARG* 1.3 55.9 + - - +
310A LEU* 3.5 8.8 + - + +
311A PHE* 3.0 29.1 + - - +
350A PHE* 4.3 18.0 - - + +
353A LEU* 3.3 39.0 - - + +
354A GLY* 3.7 16.6 - - - +
357A LEU* 3.9 20.0 - - + -
360A PHE* 3.6 46.0 - - + -
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Residues in contact with ARG 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 GLU* 2.8 20.4 + - + +
305A THR* 3.4 13.2 - - - +
306A ASN 2.9 1.2 - - - -
307A LEU* 1.3 71.2 - - - +
309A LYS* 1.3 60.9 + - + +
310A LEU 2.8 9.8 + - - -
311A PHE* 3.1 27.7 + - - +
312A ASP* 2.7 63.0 + - - +
360A PHE* 4.8 13.8 - - + -
364A LYS* 5.1 22.3 - - - +
369A LYS* 6.0 3.0 - - - +
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Residues in contact with LYS 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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263A CYS* 4.1 12.8 - - + +
264A GLU* 3.6 54.3 + - - +
267A LEU* 3.9 7.9 - - + +
268A PRO* 4.5 12.8 - - + -
305A THR* 2.8 45.0 + - - +
306A ASN* 3.1 9.1 + - - +
308A ARG* 1.3 78.4 - - + +
310A LEU* 1.3 56.0 + - - +
312A ASP* 3.9 8.9 - - - +
313A LYS* 3.3 24.4 + - - +
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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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263A CYS* 4.0 14.1 - - - -
267A LEU* 4.1 17.7 - - + -
290A LEU* 5.0 6.5 - - + -
306A ASN 3.3 9.3 + - - +
307A LEU* 3.5 11.2 - - + +
308A ARG 2.9 0.4 - - - -
309A LYS* 1.3 75.1 - - - +
311A PHE* 1.3 66.1 + - - +
312A ASP 3.1 0.9 - - - -
313A LYS* 3.1 4.7 + - - +
314A LEU* 3.0 21.7 + - + +
346A LEU* 3.6 35.3 - - + +
349A SER* 4.1 16.6 - - - -
350A PHE* 3.8 20.2 - - + +
353A LEU* 3.8 29.8 - - + -
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Residues in contact with PHE 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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307A LEU 3.0 14.6 + - - +
308A ARG* 3.3 36.6 - - - +
310A LEU* 1.3 76.3 - - - +
312A ASP* 1.3 61.3 + - - +
314A LEU* 3.2 13.2 - - + +
315A LEU* 3.2 48.7 - - + +
350A PHE* 3.4 33.2 - + + -
360A PHE* 4.2 12.3 - + + -
361A LEU* 4.4 13.5 - - + -
364A LYS 6.2 3.4 - - - -
369A LYS* 4.5 20.4 - - + -
370A LEU* 5.9 1.3 - - - -
373A PHE* 3.9 37.5 - + + -
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Residues in contact with ASP 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 ARG* 2.7 66.9 + - - +
309A LYS* 4.1 7.2 - - - +
311A PHE* 1.3 79.0 - - - +
313A LYS* 1.3 64.9 + - - +
314A LEU 3.4 0.2 + - - -
315A LEU* 3.4 15.4 + - - +
316A GLU* 3.4 23.2 + - - +
369A LYS* 5.8 3.3 - - - -
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Residues in contact with LYS 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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267A LEU* 4.0 28.3 + - + +
268A PRO* 5.3 0.6 + - + -
270A LEU* 3.4 48.2 + - + +
271A GLY 4.4 1.2 - - - +
287A LEU* 5.3 0.7 - - + -
309A LYS 3.3 16.0 + - - +
310A LEU 3.1 5.8 + - - +
312A ASP* 1.3 75.2 - - - +
314A LEU* 1.3 65.7 + - - +
316A GLU* 3.4 33.8 + - - +
317A TYR* 3.2 52.9 + - + -
346A LEU* 4.2 20.6 - - + -
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Residues in contact with LEU 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 11.5 + - + +
311A PHE* 3.2 13.9 - - - +
313A LYS* 1.3 77.6 - - - +
315A LEU* 1.3 57.5 + - + +
317A TYR* 2.9 25.1 + - - +
318A MET* 3.4 45.8 + - + +
343A VAL* 4.4 8.3 - - + -
346A LEU* 3.7 30.2 - - + +
347A LEU* 3.9 26.9 - - + +
350A PHE* 4.6 20.9 - - + -
373A PHE* 4.1 16.8 - - + -
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Residues in contact with LEU 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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311A PHE* 3.2 43.3 - - + +
312A ASP* 3.4 11.1 + - - +
314A LEU* 1.3 83.1 - - + +
316A GLU* 1.3 57.7 + - + +
317A TYR 3.0 5.6 + - - -
318A MET* 3.4 14.4 + - + +
319A PRO* 4.4 0.5 - - - +
369A LYS* 3.7 27.6 - - + +
372A ASP 5.5 0.9 - - - +
373A PHE* 3.5 37.2 - - + -
376A ARG* 3.0 48.0 + - - +
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Residues in contact with GLU 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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312A ASP* 3.4 20.0 - - - +
313A LYS* 3.4 44.2 + - - +
314A LEU 3.0 1.0 + - - -
315A LEU* 1.3 76.5 - - - +
317A TYR* 1.3 70.6 + - + +
318A MET 5.3 0.4 - - - -
319A PRO* 5.5 1.3 - - - -
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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