Contacts of the helix formed by residues 289 - 310 (chain B) in PDB entry 2CXO
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 GLY 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 3.2 27.1 - - - +
285B ALA 2.8 18.9 + - - +
288B VAL* 1.3 83.1 - - - +
290B PHE* 1.3 64.6 + - - -
291B ASP* 3.3 3.4 - - - -
292B HIS 3.3 1.8 + - - -
293B PHE* 3.1 18.5 + - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.3 47.8 - - + -
129B MET* 3.8 12.8 - - + -
130B LYS* 3.6 51.1 - - + -
133B CYS* 4.5 10.2 - - + +
137B ARG* 5.1 0.4 - - - +
285B ALA* 3.6 18.8 + - + -
289B GLY* 1.3 70.7 - - - -
291B ASP* 1.3 60.9 + - - +
293B PHE* 3.1 18.7 + + - +
294B GLU* 2.8 61.9 + - + +
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS* 5.2 9.0 + - - -
289B GLY* 3.3 0.9 - - - -
290B PHE* 1.3 78.5 - - - +
292B HIS* 1.3 59.9 + - + +
294B GLU* 3.1 20.7 + - - +
295B GLN* 3.0 40.6 + - - +
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Residues in contact with HIS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 5.4 0.4 - - - +
174B TYR* 3.6 37.4 + + + +
288B VAL* 2.8 40.3 + - + +
289B GLY 3.3 1.6 + - - -
290B PHE 3.3 0.2 - - - -
291B ASP* 1.3 78.4 - - + +
293B PHE* 1.3 60.8 + - - +
295B GLN* 3.1 34.4 + - - -
296B LEU* 2.9 25.5 + - - +
484B PRO* 3.4 26.6 - - + +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.9 17.9 - - + -
129B MET* 3.8 18.6 - - + -
276B LEU 3.7 24.7 - - - -
277B TRP 3.8 13.0 - - - -
278B SER 4.0 7.4 - - - -
281B GLY* 3.8 13.9 - - - -
284B ILE* 3.9 21.5 - - + -
285B ALA* 3.8 14.8 - - + -
288B VAL* 4.4 3.5 - - - +
289B GLY 3.1 12.8 + - - +
290B PHE* 3.1 27.5 + + - +
292B HIS* 1.3 76.3 - - - +
294B GLU* 1.3 57.1 + - - +
296B LEU* 3.2 23.1 + - + +
297B LEU* 3.0 41.5 + - + +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.0 33.9 + - - +
130B LYS* 5.3 7.9 + - - +
290B PHE* 2.8 44.5 + - + +
291B ASP* 3.1 24.7 + - - +
293B PHE* 1.3 77.0 - - - +
295B GLN* 1.3 56.5 + - + +
297B LEU* 3.3 10.8 + - + +
298B SER* 2.9 33.6 + - - +
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Residues in contact with GLN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ASP* 3.0 28.3 + - - +
292B HIS* 3.1 36.0 + - - +
294B GLU* 1.3 73.3 - - - +
296B LEU* 1.3 65.9 + - - +
298B SER* 3.2 8.6 + - - -
299B GLY 3.0 19.1 + - - -
484B PRO* 4.0 14.9 - - + +
485B PHE* 3.3 23.1 + - + +
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Residues in contact with LEU 296 (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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167B VAL* 4.1 17.0 - - + -
171B LEU* 4.5 3.8 - - + -
276B LEU* 3.9 24.7 - - + -
277B TRP* 3.7 12.8 - - + -
284B ILE* 4.5 3.4 - - + -
292B HIS 2.9 12.9 + - - +
293B PHE* 3.2 32.3 - - + +
295B GLN* 1.3 76.8 - - - +
297B LEU* 1.3 61.7 + - + +
299B GLY 3.4 0.7 + - - -
300B ALA 3.2 16.1 + - - -
484B PRO* 3.3 25.2 + - + +
487B LEU* 4.2 20.2 - - + -
488B GLY* 3.5 27.7 - - - +
491B ILE* 4.6 4.0 - - + -
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Residues in contact with LEU 297 (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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103B LEU 4.1 8.1 - - - +
104B ARG* 3.4 30.9 - - + +
106B ARG* 4.0 26.9 - - - +
126B LEU* 4.0 17.3 - - + -
277B TRP* 3.5 42.4 - - + +
293B PHE* 3.0 42.0 + - + +
294B GLU* 3.6 12.1 - - + +
296B LEU* 1.3 76.0 - - + +
298B SER* 1.3 57.5 + - - +
300B ALA 3.2 2.1 + - - -
301B HIS* 2.9 24.8 + - - +
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.6 28.3 + - - +
294B GLU* 2.9 21.3 + - - +
295B GLN* 3.2 8.4 + - - -
297B LEU* 1.3 74.1 - - - +
299B GLY* 1.3 59.9 + - - +
301B HIS* 3.3 2.8 + - - +
302B TRP* 2.9 23.7 + - - +
485B PHE* 3.6 19.4 - - - -
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLN 3.0 9.9 + - - -
296B LEU 3.4 0.9 + - - -
297B LEU 3.3 0.2 - - - -
298B SER* 1.3 72.9 - - - +
300B ALA* 1.3 65.6 + - - +
302B TRP* 3.3 3.5 + - - +
303B MET 3.2 16.8 + - - -
485B PHE* 3.2 41.4 - - - -
489B ALA* 3.3 18.4 - - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 3.7 19.3 - - - +
277B TRP* 3.4 37.5 - - + -
296B LEU 3.2 4.9 + - - -
297B LEU 3.2 8.3 + - - +
299B GLY* 1.3 75.3 - - - +
301B HIS* 1.3 56.7 + - - +
303B MET* 3.2 3.5 + - - +
304B ASP* 2.8 35.6 + - - +
488B GLY 3.5 11.4 - - - +
492B ALA* 3.7 7.3 - - + +
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Residues in contact with HIS 301 (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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101B VAL 5.2 1.0 + - - -
104B ARG* 3.2 25.6 + - - +
105B ASN* 3.4 27.9 - - + -
106B ARG* 3.7 22.7 - - + -
107B SER* 3.6 19.2 + - - -
297B LEU 2.9 10.1 + - - +
298B SER 3.5 8.5 - - - +
299B GLY 3.3 0.2 - - - -
300B ALA* 1.3 72.4 - - - +
302B TRP* 1.3 66.7 + - - +
304B ASP* 3.2 13.8 + - - +
305B GLN* 2.9 54.3 + - + +
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Residues in contact with TRP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.9 25.8 - - + -
45B ASN 3.5 20.3 + - - -
46B THR* 3.5 48.7 + - + +
51B ILE* 5.5 0.2 - - + -
298B SER 2.9 14.1 + - - +
299B GLY 3.5 9.4 - - - +
300B ALA 3.3 0.4 - - - -
301B HIS* 1.3 76.9 - - - +
303B MET* 1.3 82.1 + - + +
305B GLN* 3.2 8.7 + - + +
306B HIS* 2.9 52.9 + + + -
485B PHE* 3.8 12.6 - + + -
489B ALA* 5.0 1.8 - - + -
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Residues in contact with MET 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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44B LEU* 4.3 12.8 - - + -
51B ILE* 4.3 9.0 - - + -
299B GLY 3.2 7.9 + - - +
300B ALA 3.6 6.7 - - - +
302B TRP* 1.3 97.8 - - + +
304B ASP* 1.3 61.1 + - - +
306B HIS* 3.3 23.2 + - - +
307B PHE* 2.9 29.2 + - - +
316B ALA* 4.9 0.4 - - - -
317B PRO* 4.3 4.9 - - + -
489B ALA* 3.5 38.1 - - + +
492B ALA* 3.8 8.1 - - + +
493B MET* 3.5 40.2 - - + +
496B HIS* 4.6 3.4 - - + -
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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
----------------------------------------------------------
85B PHE* 3.5 18.7 - - + -
101B VAL* 3.7 16.4 - - + +
104B ARG* 2.7 45.9 + - - +
300B ALA 2.8 14.8 + - - +
301B HIS* 3.4 15.4 + - - +
303B MET* 1.3 73.9 - - - +
305B GLN* 1.3 59.7 + - - +
307B PHE* 3.3 3.5 + - - +
308B LEU* 2.9 29.5 + - - +
492B ALA* 4.2 0.7 - - - +
496B HIS* 2.7 32.1 + - - -
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Residues in contact with GLN 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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85B PHE* 4.9 5.5 - - - -
107B SER* 5.8 1.1 + - - -
301B HIS* 2.9 47.0 + - + +
302B TRP* 3.5 11.2 - - + +
304B ASP* 1.3 76.6 - - - +
306B HIS* 1.3 65.6 + - - +
308B LEU* 4.1 21.8 - - - +
309B LYS* 2.9 57.2 + - + +
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Residues in contact with HIS 306 (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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44B LEU* 3.5 28.8 - - + +
302B TRP* 2.9 37.7 + + + +
303B MET* 3.5 16.6 - - - +
305B GLN* 1.3 75.3 - - - +
307B PHE* 1.3 62.8 + - - +
309B LYS* 5.2 0.7 - - - -
310B THR* 2.7 51.3 + - + -
314B LYS 3.8 13.9 - - - -
315B ASN* 3.7 3.7 - - - -
316B ALA* 3.0 32.7 + - + +
317B PRO* 3.8 14.1 - - + -
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Residues in contact with PHE 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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77B VAL* 5.1 2.9 - - + -
81B ARG* 2.8 49.4 + - + -
84B MET* 4.3 1.6 - - + -
85B PHE* 3.9 13.7 - + - -
303B MET 2.9 20.8 + - - +
304B ASP 3.5 2.9 - - - +
306B HIS* 1.3 73.3 - - - +
308B LEU* 1.3 57.6 + - - +
315B ASN* 3.0 31.7 + - - +
317B PRO* 3.7 11.2 - - + -
318B VAL* 3.7 21.3 - - + -
496B HIS* 3.2 48.2 - + + -
499B PHE* 3.7 28.0 - + - -
500B VAL* 3.7 13.7 - - + -
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Residues in contact with LEU 308 (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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81B ARG* 3.4 30.0 + - - +
82B ASP* 3.7 24.0 - - - +
85B PHE* 3.8 42.0 - - + -
304B ASP 2.9 16.0 + - - +
305B GLN* 3.7 24.7 - - - +
306B HIS 3.2 0.2 - - - -
307B PHE* 1.3 78.1 - - - +
309B LYS* 1.3 63.8 + - + +
310B THR 3.6 0.2 - - - -
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Residues in contact with LYS 309 (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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305B GLN* 2.9 46.4 + - + +
306B HIS* 4.7 0.4 - - - +
308B LEU* 1.3 85.9 - - + +
310B THR* 1.3 64.2 + - - +
311B PRO* 3.7 6.6 - - - +
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Residues in contact with THR 310 (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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78B GLU* 5.3 0.7 - - - +
81B ARG* 4.3 7.6 + - - -
306B HIS* 2.7 44.9 + - + -
308B LEU 3.6 0.4 - - - -
309B LYS* 1.3 78.7 - - - +
311B PRO* 1.3 82.9 - - + +
312B LEU* 3.4 1.9 + - - +
314B LYS* 3.4 43.3 - - + +
315B ASN* 2.9 23.4 + - - -
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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
------------------------------------------------------------
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