Contacts of the helix formed by residues 299 - 315 (chain A) in PDB entry 5E3H
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 GLN 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ALA* 3.3 2.4 - - - +
298A ASN* 1.3 98.5 + - - +
300A ILE* 1.3 61.0 + - - +
301A PRO* 4.2 7.9 - - + -
302A VAL* 3.2 28.1 + - + +
303A TYR* 2.8 28.4 + - - +
347A THR* 5.8 0.4 - - - -
373A GLU* 5.7 1.6 - - - +
699A VAL 4.7 5.5 - - - +
701A ASP 3.9 12.5 + - - +
702A GLU* 3.8 26.2 + - - +
703A GLY 4.0 8.3 + - - -
704A ILE* 5.8 4.2 - - - +
11C G 5.1 1.4 + - - -
12C U 4.0 30.9 - - - +
13C C 3.8 4.9 - - - -
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Residues in contact with ILE 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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299A GLN* 1.3 71.0 - - - +
301A PRO* 1.3 66.4 - - + +
303A TYR* 3.0 9.5 + - + +
304A GLU* 2.9 41.5 + - + +
325A SER* 4.1 17.9 - - - +
326A GLY 4.9 0.2 - - - +
347A THR* 4.4 6.1 - - - +
664A ARG* 4.8 5.4 - - - +
675A LEU* 4.0 20.9 - - + -
13C C 2.8 35.1 + - - +
14C G 3.6 33.2 - - - +
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Residues in contact with PRO 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLN* 3.5 8.7 - - + -
300A ILE* 1.3 96.6 - - + +
302A VAL* 1.3 62.5 + - + +
304A GLU* 3.4 8.0 + - + +
305A GLN* 3.1 23.2 + - - +
664A ARG* 5.1 1.1 - - - +
675A LEU* 4.5 24.2 - - + -
678A GLN* 5.7 3.1 - - - +
704A ILE* 4.3 29.8 - - + -
13C C 3.8 6.5 - - - +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA* 4.0 13.0 - - + -
298A ASN* 5.7 0.4 - - - +
299A GLN* 3.2 35.8 + - + +
301A PRO* 1.3 77.2 - - + +
303A TYR* 1.3 64.2 + - - +
305A GLN* 3.4 7.2 + - + +
306A GLN* 3.1 38.0 + - + +
372A ASP* 3.9 21.5 - - - +
703A GLY 4.2 13.5 - - - +
704A ILE* 5.4 4.9 - - + -
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA* 3.9 15.9 - - + +
299A GLN 2.8 14.3 + - - +
300A ILE* 3.3 15.0 - - + +
302A VAL* 1.3 77.3 - - - +
304A GLU* 1.3 82.1 + - + +
307A LYS* 3.2 37.0 + - + +
323A GLY* 3.0 12.2 + - - -
324A ILE* 3.0 33.7 + - - -
325A SER* 3.6 27.5 + - - -
328A THR* 4.6 1.7 + - - +
345A ILE* 3.5 45.1 - - + +
346A LEU 4.3 9.0 - - - -
347A THR* 4.6 6.5 - - - +
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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
----------------------------------------------------------
300A ILE* 2.9 33.5 + - + +
301A PRO* 3.9 6.9 - - - +
303A TYR* 1.3 94.7 - - + +
305A GLN* 1.3 61.7 + - - +
307A LYS* 3.6 5.8 + - - +
308A SER* 3.1 22.2 + - - -
675A LEU* 5.7 2.3 - - - +
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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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271A THR* 5.3 4.8 + - - +
301A PRO 3.1 17.2 + - - +
302A VAL* 3.8 8.0 - - - +
303A TYR 3.3 0.2 - - - -
304A GLU* 1.3 74.7 - - - +
306A GLN* 1.3 79.8 + - - +
308A SER* 3.1 8.8 + - - -
309A VAL* 3.0 32.5 + - + +
704A ILE 4.7 9.8 - - - +
705A ASP* 5.0 15.2 + - - +
1006A ADP 5.5 7.7 + - - -
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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
----------------------------------------------------------
271A THR* 3.4 34.2 + - - +
295A PHE* 3.2 42.7 - - + -
297A ALA* 5.1 0.4 - - + -
302A VAL* 3.1 34.1 + - + +
303A TYR 4.0 2.7 - - - +
305A GLN* 1.3 92.0 - - - +
307A LYS* 1.3 60.3 + - - +
308A SER 3.1 0.2 + - - -
309A VAL* 3.2 3.8 + - - +
310A PHE* 2.9 55.3 + - + +
345A ILE* 4.3 10.3 - - + -
372A ASP* 6.1 0.9 - - - -
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Residues in contact with LYS 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 TYR* 3.2 41.1 + - + +
304A GLU* 3.8 5.8 - - - +
305A GLN 3.3 0.2 - - - -
306A GLN* 1.3 78.6 - - - +
308A SER* 1.3 58.2 + - - +
311A SER* 2.8 43.6 + - - +
321A VAL* 4.3 2.4 + - - +
322A THR* 4.3 9.7 + - - +
323A GLY* 4.1 22.1 - - - +
345A ILE* 3.6 26.8 - - + +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU 3.1 13.6 + - - -
305A GLN* 3.1 11.8 + - - -
306A GLN 3.1 0.4 - - - -
307A LYS* 1.3 75.3 - - - +
309A VAL* 1.3 67.1 + - - +
311A SER* 3.4 3.6 + - - -
312A LYS* 3.0 25.6 + - - +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 5.1 8.5 - - + -
275A LEU* 3.7 30.5 - - + -
305A GLN* 3.0 28.3 + - + +
306A GLN* 3.9 9.0 - - - +
308A SER* 1.3 76.5 - - - +
310A PHE* 1.3 62.2 + - + +
312A LYS* 3.3 5.9 + - - +
313A TYR* 2.9 34.0 + - + +
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Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 4.9 2.7 - - + -
274A SER* 3.9 11.2 - - - -
275A LEU* 3.4 26.9 - - + -
278A CYS* 4.3 15.5 - - + -
293A VAL* 5.8 0.7 - - + -
295A PHE* 3.5 32.5 - + + -
306A GLN* 2.9 54.8 + - + +
307A LYS 4.3 0.2 - - - +
309A VAL* 1.3 80.2 - - + +
311A SER* 1.3 58.1 + - - +
313A TYR* 4.5 1.1 - - - -
314A PHE* 2.9 57.6 + + + +
321A VAL* 3.5 17.1 - - + +
343A ILE* 3.8 19.3 - - + -
345A ILE* 4.2 6.1 - - + -
370A ILE* 5.4 1.3 - - + -
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LYS* 2.8 33.5 + - - +
308A SER* 3.8 4.3 - - - -
309A VAL 3.2 0.2 - - - -
310A PHE* 1.3 77.2 - - - +
312A LYS* 1.3 61.6 + - - +
315A GLU* 3.2 32.8 + - - +
321A VAL* 3.3 31.8 + - - +
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Residues in contact with LYS 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 SER* 3.0 17.7 + - - +
309A VAL* 3.8 4.3 - - - +
311A SER* 1.3 77.8 - - - +
313A TYR* 1.3 61.6 + - - +
315A GLU* 4.3 3.5 + - - +
316A ARG* 3.9 26.2 + - - +
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Residues in contact with TYR 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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272A PHE* 4.5 25.5 - + - -
275A LEU* 4.5 19.9 + - + -
276A LEU* 4.9 3.8 - - - +
279A GLU* 3.1 31.4 + - + -
309A VAL* 2.9 20.1 + - + +
310A PHE* 3.9 3.8 - - - +
312A LYS* 1.3 81.2 - - - +
314A PHE* 1.3 90.7 + + + +
315A GLU 3.6 0.7 + - - -
316A ARG* 4.0 12.4 - - - +
317A HIS* 3.4 36.0 + + - -
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Residues in contact with PHE 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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275A LEU* 3.5 45.3 - - + -
278A CYS* 3.8 9.6 - - + -
279A GLU* 3.6 34.1 - - + -
282A LEU* 4.6 1.8 - - + -
310A PHE* 2.9 38.7 + + - +
313A TYR* 1.3 92.2 - + - +
315A GLU* 1.3 63.9 + - - +
316A ARG 3.2 2.5 - - - -
317A HIS* 3.4 13.5 + - - -
319A TYR* 3.1 42.1 + + + +
321A VAL* 3.9 5.8 - - + -
343A ILE* 3.3 30.1 - - + -
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Residues in contact with GLU 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 SER* 3.2 23.2 + - - +
312A LYS* 4.6 5.4 - - - +
313A TYR 3.4 0.6 - - - -
314A PHE* 1.3 77.7 - - - +
316A ARG* 1.3 64.7 + - + +
318A GLY* 3.3 12.5 + - - -
319A TYR 4.0 12.3 + - - +
320A ARG* 4.9 3.1 - - - -
321A VAL* 4.8 7.5 + - - +
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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