Contacts of the helix formed by residues 302 - 316 (chain A) in PDB entry 2EIT
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 ASP 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ALA* 1.3 71.5 - - - +
303A PHE* 1.3 57.8 + - - +
304A ASP* 3.2 12.6 + - - +
305A LEU* 3.1 40.8 + - + +
306A ALA* 2.8 29.5 + - - +
450A TYR* 4.6 1.6 - - - +
452A ARG* 3.5 28.6 + - + +
472A ASN* 5.7 1.8 + - - -
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Residues in contact with PHE 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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298A ASP 3.5 22.4 - - - -
299A GLU* 3.5 26.0 - - - -
301A ALA* 3.2 19.9 + - + -
302A ASP* 1.3 72.5 + - - +
304A ASP* 1.3 57.9 + - - +
306A ALA* 3.7 4.6 - - - +
307A ALA* 3.0 28.4 + - - +
333A GLY 4.3 10.5 - - - -
334A ALA* 4.2 3.6 - - + -
337A PRO* 3.5 27.1 - - + -
338A VAL* 3.4 28.8 - - + +
341A ARG* 3.7 29.4 - - - +
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Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASP* 3.2 9.2 + - - +
303A PHE* 1.3 75.4 - - - +
305A LEU* 1.3 64.0 + - - +
307A ALA* 3.3 2.7 + - - +
308A GLU* 3.1 20.1 + - - +
341A ARG* 2.9 33.7 + - - +
345A ARG* 3.5 20.6 + - - +
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Residues in contact with LEU 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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302A ASP* 3.1 34.1 + - + +
304A ASP* 1.3 77.6 - - - +
306A ALA* 1.3 61.5 + - - +
308A GLU* 3.4 9.2 + - + +
309A GLY 3.1 18.2 + - - -
450A TYR* 3.6 20.3 + - + +
472A ASN* 3.9 29.2 - - + +
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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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297A VAL* 4.1 21.3 - - + -
302A ASP 2.8 17.2 + - - +
303A PHE* 3.7 6.5 - - - +
304A ASP 3.3 0.2 - - - -
305A LEU* 1.3 77.8 - - - +
307A ALA* 1.3 64.0 + - - +
309A GLY* 3.2 1.7 + - - -
310A VAL* 2.9 29.3 + - - +
338A VAL* 4.9 3.4 - - + -
450A TYR* 3.5 37.7 - - + -
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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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303A PHE 3.0 18.4 + - - +
304A ASP* 3.8 5.6 - - - +
305A LEU 3.3 0.2 - - - -
306A ALA* 1.3 76.3 - - - +
308A GLU* 1.3 63.1 + - - +
310A VAL* 3.4 1.2 + - - +
311A VAL* 3.0 30.0 + - - +
338A VAL* 4.7 2.4 - - + +
341A ARG* 3.5 37.2 - - + -
342A VAL* 4.0 15.3 - - + +
345A ARG* 4.0 10.8 - - - +
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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 ASP 3.1 13.6 + - - +
305A LEU* 3.7 12.2 - - + +
307A ALA* 1.3 76.5 - - - +
309A GLY* 1.3 68.0 + - - +
311A VAL* 3.3 4.1 + - - +
312A VAL* 3.0 45.7 + - - +
345A ARG* 3.5 34.0 - - - +
1531A MPD 4.5 10.5 + - - +
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Residues in contact with GLY 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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295A ILE* 4.6 2.7 - - - -
305A LEU 3.1 11.7 + - - -
306A ALA 3.7 0.2 - - - -
308A GLU* 1.3 82.6 + - - +
310A VAL* 1.3 55.3 + - - +
312A VAL* 3.5 5.0 + - - +
313A SER* 2.7 38.4 + - - -
450A TYR* 3.2 24.5 - - - -
474A LYS* 4.2 7.8 - - - +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 4.0 27.6 - - + -
297A VAL* 4.7 3.6 - - + -
306A ALA* 2.9 24.2 + - - +
307A ALA 3.7 4.0 - - - +
309A GLY* 1.3 76.5 - - - +
311A VAL* 1.3 58.2 + - - +
313A SER* 3.2 1.2 + - - -
314A ALA* 2.8 30.0 + - - +
315A TYR* 6.2 0.2 - - + -
325A ALA* 4.6 1.7 - - + +
328A LEU* 3.7 30.1 - - + -
338A VAL* 5.3 0.7 - - + -
342A VAL* 4.1 19.3 - - + -
423A LEU* 3.9 31.2 - - + -
450A TYR* 4.9 0.7 - - + -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA 3.0 17.8 + - - +
308A GLU* 3.8 5.4 - - - +
310A VAL* 1.3 76.4 - - - +
312A VAL* 1.3 62.1 + - - +
315A TYR* 3.0 33.4 + - + +
316A GLY 4.1 0.2 + - - -
342A VAL* 4.0 24.9 - - + +
345A ARG* 3.9 26.7 - - + -
346A ALA* 4.3 6.7 - - + +
349A LEU* 3.9 37.2 - - + -
1531A MPD 4.2 10.5 - - - +
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Residues in contact with VAL 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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130A GLU* 5.9 1.8 - - - +
308A GLU* 3.0 39.5 + - - +
309A GLY* 3.8 5.8 - - - +
311A VAL* 1.3 75.0 - - - +
313A SER* 1.3 59.1 + - - +
316A GLY* 3.0 29.1 + - - -
321A LYS* 5.6 0.3 + - - -
474A LYS* 3.8 29.4 - - + -
476A THR* 4.4 7.7 + - - +
1531A MPD 3.9 36.3 - - + +
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 3.8 7.2 - - - +
309A GLY 2.7 24.0 + - - -
310A VAL 3.7 1.8 - - - -
312A VAL* 1.3 76.8 - - - +
314A ALA* 1.3 60.9 + - - +
316A GLY* 4.7 2.1 + - - +
321A LYS* 5.7 0.2 - - - +
324A ALA* 3.3 12.3 - - - +
325A ALA* 3.0 35.7 + - - -
474A LYS* 3.3 5.5 - - - +
475A ILE* 3.0 33.7 + - - -
476A THR* 3.7 13.3 - - - +
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Residues in contact with ALA 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 VAL 2.8 21.0 + - - +
313A SER* 1.3 74.5 - - - +
315A TYR* 1.3 89.1 + - + +
316A GLY 3.8 0.2 - - - -
319A GLY* 3.3 21.5 - - - -
324A ALA* 4.6 1.2 - - - +
325A ALA* 3.2 23.9 - - + +
420A GLY 4.5 3.8 - - - +
421A PRO* 4.5 0.2 - - - +
422A VAL 5.0 1.5 + - - -
423A LEU* 4.1 18.2 - - + +
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Residues in contact with TYR 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 VAL* 3.0 30.4 + - + +
314A ALA* 1.3 97.5 - - + +
316A GLY* 1.3 62.0 + - - +
317A PHE 3.4 0.5 + - - -
318A GLN* 2.9 22.3 + - - +
319A GLY 4.1 2.0 - - - +
342A VAL* 5.5 1.1 - - + -
346A ALA* 4.0 18.4 - - + -
349A LEU* 3.8 16.8 - - + -
359A ASP 4.6 0.3 - - - +
360A LEU* 3.7 20.6 - - + +
401A PRO* 3.9 12.6 - - + -
402A THR 2.8 25.2 + - - -
403A VAL* 3.1 20.1 - - + +
421A PRO* 3.4 41.1 - - + -
422A VAL 4.2 1.1 - - - -
423A LEU* 3.5 10.6 - - + +
1531A MPD 3.7 13.2 - - + +
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.6 15.7 - - - -
312A VAL* 3.0 19.8 + - - -
313A SER 4.6 1.8 - - - +
314A ALA 3.8 0.7 - - - -
315A TYR* 1.3 75.5 - - - +
317A PHE* 1.3 69.6 + - - +
319A GLY* 3.0 13.2 + - - -
320A GLN 4.2 0.5 + - - -
321A LYS* 3.8 16.0 - - - +
324A ALA* 5.6 0.2 - - - +
359A ASP 5.5 0.2 - - - -
1531A MPD 3.7 14.3 - - - +
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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