Contacts of the helix formed by residues 302 - 316 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ALA* 1.3 69.8 - - - +
303B PHE* 1.3 57.7 + - - +
304B ASP* 3.2 12.6 + - - +
305B LEU* 3.0 41.4 + - + +
306B ALA* 2.8 28.8 + - - +
450B TYR* 4.7 1.8 - - - +
452B ARG* 3.5 30.3 + - + +
472B ASN* 5.6 2.2 + - - -
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ASP 3.5 22.9 - - - -
299B GLU* 3.6 23.6 - - + -
301B ALA* 3.2 18.3 + - + -
302B ASP* 1.3 72.6 + - - +
304B ASP* 1.3 57.6 + - - +
306B ALA* 3.7 4.9 - - - +
307B ALA* 2.9 30.0 + - - +
333B GLY 4.2 11.9 - - - -
334B ALA* 4.1 3.8 - - + -
337B PRO* 3.5 27.1 - - + -
338B VAL* 3.4 29.3 - - + +
341B ARG* 3.8 27.3 - - - +
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Residues in contact with ASP 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASP* 3.2 8.6 + - - +
303B PHE* 1.3 74.3 - - - +
305B LEU* 1.3 65.9 + - - +
307B ALA* 3.4 4.0 + - - +
308B GLU* 3.1 24.4 + - - +
341B ARG* 2.8 37.3 + - - +
345B ARG* 4.3 9.6 + - - +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASP* 3.0 35.5 + - + +
304B ASP* 1.3 77.2 - - - +
306B ALA* 1.3 63.2 + - - +
308B GLU* 3.4 8.7 + - + +
309B GLY 3.1 18.5 + - - -
450B TYR* 3.7 16.0 + - + +
472B ASN* 3.8 30.5 - - + +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 4.0 23.6 - - + -
302B ASP 2.8 17.2 + - - +
303B PHE* 3.7 6.1 - - - +
305B LEU* 1.3 75.8 - - - +
307B ALA* 1.3 56.7 + - - +
309B GLY* 3.2 1.9 + - - -
310B VAL* 2.9 34.9 + - - +
338B VAL* 4.9 4.0 - - + -
450B TYR* 3.5 35.9 - - + -
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE 2.9 19.0 + - - +
304B ASP* 3.8 4.9 - - - +
305B LEU 3.4 0.2 - - - -
306B ALA* 1.3 75.8 - - - +
308B GLU* 1.3 63.7 + - - +
310B VAL* 3.4 1.2 + - - +
311B VAL* 3.0 30.5 + - - +
338B VAL* 4.6 2.2 - - + +
341B ARG* 3.6 28.7 - - + -
342B VAL* 3.8 25.1 - - + +
345B ARG* 3.9 9.2 - - - +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ASP 3.1 17.2 + - - +
305B LEU* 3.7 9.0 - - + +
307B ALA* 1.3 76.2 - - - +
309B GLY* 1.3 67.8 + - - +
311B VAL* 3.3 3.7 + - - +
312B VAL* 3.1 40.2 + - - +
345B ARG* 3.3 38.6 + - - +
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 4.5 2.9 - - - -
305B LEU 3.1 10.9 + - - -
306B ALA 3.7 0.2 - - - -
308B GLU* 1.3 82.8 + - - +
310B VAL* 1.3 54.4 + - - +
312B VAL* 3.9 5.0 - - - +
313B SER* 2.7 39.1 + - - -
450B TYR* 3.2 23.6 - - - -
474B LYS* 4.2 7.6 - - - -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.9 28.7 - - + -
297B VAL* 4.7 4.0 - - + -
306B ALA 2.9 23.3 + - - +
307B ALA* 3.8 4.9 - - - +
309B GLY* 1.3 77.7 - - - +
311B VAL* 1.3 57.1 + - - +
313B SER* 3.3 1.2 + - - -
314B ALA* 2.8 29.6 + - - +
325B ALA* 4.6 1.5 - - + +
328B LEU* 3.7 29.6 - - + -
338B VAL* 5.3 0.7 - - + -
342B VAL* 4.1 18.6 - - + -
423B LEU* 3.9 30.5 - - + -
450B TYR* 4.7 1.1 - - + -
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 3.0 20.9 + - - +
308B GLU* 3.9 4.9 - - - +
310B VAL* 1.3 73.3 - - - +
312B VAL* 1.3 66.9 + - + +
315B TYR* 3.0 33.1 + - + +
316B GLY 4.1 0.2 + - - -
342B VAL* 4.0 24.9 - - + +
345B ARG* 3.9 27.4 - - + +
346B ALA* 4.2 6.7 - - + +
349B LEU* 3.8 37.7 - - + -
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 6.1 1.3 - - - +
308B GLU* 3.1 39.4 + - - +
309B GLY* 3.9 5.8 - - - +
311B VAL* 1.3 77.9 - - + +
313B SER* 1.3 59.6 + - - +
316B GLY* 3.0 30.5 + - - +
321B LYS* 5.7 0.5 + - - -
474B LYS* 3.9 30.1 - - + -
476B THR* 4.6 6.7 + - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.8 6.9 - - - +
309B GLY 2.7 23.4 + - - -
310B VAL 3.8 0.9 - - - -
312B VAL* 1.3 78.8 - - - +
314B ALA* 1.3 59.6 + - - +
316B GLY 4.6 2.4 + - - +
321B LYS* 5.6 0.2 - - - +
324B ALA* 3.4 12.1 - - - +
325B ALA* 3.0 35.2 + - - -
474B LYS* 3.3 5.7 - - - +
475B ILE* 3.0 34.9 + - - -
476B THR* 3.7 12.6 - - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL 2.8 21.3 + - - +
313B SER* 1.3 73.9 - - - +
315B TYR* 1.3 86.9 + - + +
316B GLY 3.7 0.2 - - - -
319B GLY* 3.2 23.1 + - - -
324B ALA* 4.6 1.0 - - - +
325B ALA* 3.2 24.7 + - + +
420B GLY 4.6 0.9 - - - +
421B PRO* 4.5 2.4 - - - +
422B VAL 5.1 1.7 + - - -
423B LEU* 4.2 17.5 - - + -
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Residues in contact with TYR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B VAL* 6.3 0.2 - - + -
311B VAL* 3.0 31.0 + - + +
314B ALA* 1.3 97.8 - - + +
316B GLY* 1.3 67.2 + - - +
317B PHE 3.3 0.5 + - - -
318B GLN* 3.0 14.9 + - - -
319B GLY 4.0 2.0 - - - +
342B VAL* 5.6 0.9 - - + -
346B ALA* 4.0 18.8 - - + -
349B LEU* 3.7 19.5 - - + -
359B ASP 4.5 1.9 - - - +
360B LEU* 3.7 26.5 - - + +
401B PRO* 3.9 10.3 - - + -
402B THR 2.8 25.1 + - - -
403B VAL* 3.1 19.3 - - + +
421B PRO* 3.4 40.6 - - + -
422B VAL 4.2 1.3 - - - -
423B LEU* 3.6 11.4 - - + +
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 3.7 15.3 - - - -
311B VAL 4.1 0.2 + - - -
312B VAL* 3.0 23.2 + - - +
313B SER 4.6 2.2 - - - +
314B ALA 3.7 0.6 - - - -
315B TYR* 1.3 76.1 - - - +
317B PHE* 1.3 67.3 + - - +
319B GLY* 3.0 12.5 + - - -
321B LYS* 3.7 17.1 - - - +
359B ASP 5.4 2.5 - - - -
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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