Contacts of the helix formed by residues 287 - 307 (chain B) in PDB entry 2EYQ
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 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PRO* 5.6 0.3 - - - +
286B GLY* 1.3 74.4 - - - +
288B LEU* 1.3 65.9 + - - +
289B GLU* 3.1 4.8 + - - +
290B THR* 2.4 32.0 + - - +
291B SER* 3.3 21.7 + - - -
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.6 15.5 - - + +
47B PRO* 5.2 4.3 - - + -
110B VAL* 4.5 23.7 - - + +
284B ASN* 3.3 28.9 - - + -
285B THR* 4.2 3.1 - - - +
286B GLY* 3.5 29.8 - - - +
287B ASP* 1.3 77.9 - - - +
289B GLU* 1.3 58.0 + - - +
291B SER* 3.8 4.4 - - - -
292B ALA* 2.8 33.6 + - - +
328B PHE* 4.3 11.4 - - + -
331B LEU* 4.8 8.1 - - + -
336B ARG* 3.6 25.4 - - - +
338B GLN* 5.4 1.8 - - + -
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP* 3.1 3.0 - - - +
288B LEU* 1.3 77.9 - - - +
290B THR* 1.3 66.2 + - - +
292B ALA* 3.8 1.3 - - - +
293B GLU* 3.0 27.5 + - + +
324B VAL* 5.0 7.1 - - + +
328B PHE* 3.7 31.2 - - + -
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP* 2.4 39.7 + - - +
288B LEU 3.4 0.4 - - - -
289B GLU* 1.3 78.6 - - - +
291B SER* 1.3 64.7 + - - +
293B GLU* 4.1 3.1 - - - +
294B ARG* 3.1 23.5 + - + +
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 3.2 29.6 + - - -
48B ASP* 3.6 10.8 + - - -
110B VAL* 4.4 9.4 - - - +
111B ASN* 5.2 1.4 + - - +
287B ASP 3.3 14.1 + - - -
288B LEU* 3.8 5.6 - - - -
290B THR* 1.3 77.7 - - - +
292B ALA* 1.3 70.4 + - - +
294B ARG* 2.9 29.4 + - - +
295B PHE* 3.1 7.1 + - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.4 6.4 - - + +
114B MET* 3.9 28.6 - - - +
288B LEU* 2.8 24.0 + - + +
289B GLU* 3.8 5.4 - - - +
291B SER* 1.3 70.8 - - - +
293B GLU* 1.3 67.4 + - - +
295B PHE* 2.9 17.3 + - - +
296B GLN* 3.2 8.7 + - - +
324B VAL* 4.1 13.7 - - + -
327B LEU* 4.2 12.1 - - + -
328B PHE* 4.5 5.2 - - + -
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLU* 3.0 21.4 + - + +
290B THR* 4.1 3.1 - - - +
292B ALA* 1.3 78.1 - - - +
294B ARG* 1.3 66.2 + - - +
295B PHE 3.1 0.5 + - - -
296B GLN* 3.1 26.8 + - - +
297B ALA* 3.3 17.8 + - + +
324B VAL* 3.8 22.6 - - + +
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Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.0 31.9 + - - -
290B THR* 3.1 14.0 + - + +
291B SER* 2.9 23.0 + - - +
293B GLU* 1.3 80.0 - - - +
295B PHE* 1.3 57.2 - - - +
297B ALA* 3.8 4.5 + - - +
298B ASP* 2.7 36.1 + - - +
806B ILE* 5.6 9.1 + - - +
807B LEU* 6.0 6.5 - - - +
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Residues in contact with PHE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 4.3 23.8 - - + -
111B ASN* 3.2 55.0 - - + -
114B MET* 3.8 14.8 - - + -
291B SER 3.1 5.0 + - - +
292B ALA* 2.9 13.1 + - - +
294B ARG* 1.3 78.6 - - - +
296B GLN* 1.3 65.2 + - - +
298B ASP* 2.8 22.3 + - + +
299B THR* 3.0 22.1 + - - -
321B TRP* 3.7 30.5 - + - -
807B LEU* 5.9 8.5 - - + -
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Residues in contact with GLN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B MET* 4.4 8.4 - - + +
292B ALA 3.2 7.1 + - - +
293B GLU* 3.1 20.6 + - - +
295B PHE* 1.3 78.4 - - - +
297B ALA* 1.3 63.6 + - - +
299B THR* 2.9 20.4 + - - -
300B LEU* 3.0 14.5 + - + +
322B LEU 5.6 0.9 - - - +
323B ARG* 3.4 39.6 - - - +
324B VAL* 3.0 33.0 + - + +
325B ASP* 4.6 3.6 + - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU* 3.3 14.0 + - + +
294B ARG* 4.0 8.7 - - - +
295B PHE 3.2 0.6 - - - -
296B GLN* 1.3 79.9 - - - +
298B ASP* 1.3 56.4 + - - +
299B THR 3.0 0.5 + - - -
300B LEU* 3.0 12.1 + - + +
301B ALA* 2.7 36.6 + - - +
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Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 5.4 2.2 - - + -
294B ARG* 2.7 29.4 + - - +
295B PHE* 2.8 22.5 + - + +
297B ALA* 1.3 75.2 - - - +
299B THR* 1.3 58.1 + - - +
301B ALA* 3.5 7.6 - - - +
302B ARG* 2.8 38.1 + - + +
835B GLU* 5.7 3.6 - - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 4.8 4.5 - - + -
78B TYR* 4.2 3.8 - - + -
114B MET* 5.8 0.5 - - - +
295B PHE* 3.0 31.7 + - - -
296B GLN* 3.0 13.4 + - - -
298B ASP* 1.3 75.7 - - - +
300B LEU* 1.3 67.1 + - - +
302B ARG* 3.2 6.1 + - - +
303B PHE* 2.8 22.2 + - - +
317B PRO* 3.8 16.2 - - + -
321B TRP* 3.4 46.8 - - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLN* 3.0 12.2 + - + +
297B ALA* 3.5 12.1 - - - +
299B THR* 1.3 74.1 - - - +
301B ALA* 1.3 54.4 + - - +
303B PHE* 3.0 15.8 + - + +
304B GLU* 2.8 67.7 + - + +
317B PRO* 4.7 8.0 - - + +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA 2.7 21.7 + - - +
298B ASP* 3.5 11.9 - - - +
300B LEU* 1.3 74.7 - - - +
302B ARG* 1.3 59.6 + - + +
304B GLU* 3.0 10.9 + - - +
305B ASN* 2.9 28.9 + - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.9 28.6 - - - +
77B PRO* 2.8 55.5 + - - +
78B TYR* 3.8 18.8 + - + +
79B ASP* 5.8 1.0 - - - +
298B ASP* 2.8 25.2 + - + +
299B THR* 3.8 3.4 - - - +
301B ALA* 1.3 74.1 - - + +
303B PHE* 1.3 67.3 + - - +
305B ASN* 4.4 4.0 - - - +
306B ARG* 2.8 44.0 + - - +
314B LEU* 4.8 1.6 - - - -
796B MET* 5.9 3.2 - - - +
800B GLU* 3.4 29.5 + - - +
803B LEU* 6.2 1.4 - - - +
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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
----------------------------------------------------------
78B TYR* 4.1 6.8 - - - +
299B THR 2.8 14.0 + - - +
300B LEU* 3.2 13.5 - - + +
302B ARG* 1.3 75.0 - - - +
304B GLU* 1.3 74.9 + - - +
307B GLY* 2.8 33.3 + - - -
314B LEU* 4.0 29.8 - - + -
315B LEU 3.7 33.4 - - - -
316B PRO* 3.9 14.6 - - + -
317B PRO* 3.8 21.8 - - + -
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 2.8 52.6 + - + +
301B ALA* 3.0 9.9 - - - +
303B PHE* 1.3 91.5 - - - +
305B ASN* 1.3 62.4 + - - +
307B GLY* 3.9 0.3 + - - -
308B VAL* 3.9 19.1 - - - +
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Residues in contact with ASN 305 (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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301B ALA 2.9 17.9 + - - +
302B ARG* 4.3 2.7 - - - +
304B GLU* 1.3 73.4 - - - +
306B ARG* 1.3 58.1 - - - +
308B VAL* 3.1 25.5 - - - +
796B MET* 6.1 4.5 - - + -
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 3.9 22.4 + - + +
80B SER* 3.0 29.3 + - - -
302B ARG* 2.8 31.9 + - - +
305B ASN* 1.3 71.4 - - + +
307B GLY* 1.3 60.9 + - - +
308B VAL* 3.1 7.1 + - - +
309B ASP* 3.6 27.4 + - + +
312B ARG* 5.4 8.5 - - - +
314B LEU* 3.5 18.3 - - + +
800B GLU* 3.6 30.7 + - - -
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Residues in contact with GLY 307 (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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303B PHE* 2.8 27.3 + - - -
305B ASN 3.4 1.0 - - - -
306B ARG* 1.3 76.3 - - - +
308B VAL* 1.3 57.7 + - - +
309B ASP 3.1 11.5 + - - +
313B PRO* 4.5 2.6 - - - +
314B LEU* 3.2 31.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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