Contacts of the helix formed by residues 292 - 313 (chain B) in PDB entry 4WMJ
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 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ILE* 4.0 13.9 - - - -
180B ASN* 4.1 3.8 - - - +
288B SER 2.8 18.6 + - - +
290B TYR 3.6 1.4 - - - -
291B ILE* 1.3 81.7 - - - +
293B PHE* 1.3 65.6 + - - -
294B GLU* 3.2 3.6 - - - -
295B ASN* 3.2 4.4 + - - +
296B PHE* 3.1 17.8 + - - +
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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
----------------------------------------------------------
110B ARG* 6.3 0.2 - - - -
130B LEU* 3.5 45.8 - - + -
133B MET* 4.2 5.2 - - + -
134B LYS* 3.5 52.0 - - + +
137B SER* 4.6 6.7 - - - -
138B THR* 5.4 4.9 - - + +
141B ILE* 5.1 0.6 - - - +
288B SER* 3.4 24.8 + - - +
292B GLY* 1.3 72.8 - - - -
294B GLU* 1.3 60.5 + - + +
296B PHE* 3.1 22.3 + + - +
297B GLU* 2.9 62.7 + - + +
300B LEU* 5.8 0.2 - - + -
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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
----------------------------------------------------------
134B LYS* 5.8 4.7 - - - +
292B GLY 3.2 1.2 - - - -
293B PHE* 1.3 81.2 - - + +
295B ASN* 1.3 63.4 + - - +
297B GLU* 3.4 19.8 + - - +
298B LYS* 3.2 32.0 + - - +
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Residues in contact with ASN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 3.7 30.9 + - - +
291B ILE* 2.9 43.4 + - + +
292B GLY 3.2 1.6 + - - -
294B GLU* 1.3 80.5 - - - +
296B PHE* 1.3 64.4 + - - +
298B LYS* 3.2 23.7 + - - +
299B LEU* 3.0 20.3 + - - +
487B PRO* 3.5 23.0 - - + +
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Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 4.0 16.6 - - + -
133B MET* 3.8 18.4 - - + -
279B LEU 3.6 26.0 - - - -
280B TRP* 3.7 15.9 - - - -
281B SER 3.9 7.2 - - - -
284B GLY* 3.9 13.7 - - - -
287B ILE* 3.9 23.3 - - + +
288B SER* 4.1 14.6 - - - +
291B ILE* 4.3 3.9 - - - +
292B GLY 3.1 11.8 + - - +
293B PHE* 3.5 27.4 - + - +
295B ASN* 1.3 76.4 - - - +
297B GLU* 1.3 63.4 + - - +
299B LEU* 3.1 23.3 + - + +
300B LEU* 3.0 31.8 + - + +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 3.0 28.0 + - - +
134B LYS* 5.5 2.8 + - - -
293B PHE* 2.9 51.3 + - + +
294B GLU* 3.5 20.4 - - - +
295B ASN 3.2 0.2 - - - -
296B PHE* 1.3 77.3 - - - +
298B LYS* 1.3 56.9 + - + +
300B LEU* 3.2 12.8 + - + +
301B ASP* 2.7 36.1 + - - +
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 3.2 16.7 + - - +
295B ASN* 3.2 29.3 + - - +
297B GLU* 1.3 75.5 - - + +
299B LEU* 1.3 66.9 + - - +
301B ASP* 3.2 15.0 + - + +
302B GLY 3.0 18.0 + - - -
487B PRO* 3.8 14.8 - - + -
488B PHE* 3.4 21.0 - - + +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 4.2 18.6 - - + -
175B LEU* 4.7 3.8 - - + -
279B LEU* 3.9 23.8 - - + -
280B TRP* 3.8 13.6 - - + -
287B ILE* 4.6 3.1 - - + -
295B ASN 3.0 12.0 + - - +
296B PHE* 3.2 31.2 - - + +
298B LYS* 1.3 76.1 - - - +
300B LEU* 1.3 61.5 + - - +
302B GLY 3.2 1.6 + - - -
303B ALA 3.1 17.5 + - - -
487B PRO* 3.4 25.9 - - + +
490B LEU* 4.4 17.7 - - + -
491B GLY* 3.5 29.4 - - - +
494B ILE* 4.6 4.9 - - + -
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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
----------------------------------------------------------
107B LEU 4.2 8.5 - - - +
108B ARG* 3.5 23.8 - - + +
110B ARG* 4.0 29.6 - - - +
130B LEU* 3.8 28.3 - - + -
280B TRP* 3.7 38.6 - - + +
296B PHE* 3.0 31.2 + - + +
297B GLU* 3.4 13.0 - - + +
299B LEU* 1.3 77.9 - - + +
301B ASP* 1.3 57.3 + - - +
303B ALA* 3.3 1.2 + - - +
304B ASN* 2.9 29.1 + - - +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 2.8 44.7 + - + +
297B GLU* 2.7 24.6 + - - +
298B LYS* 3.2 18.4 + - - +
300B LEU* 1.3 72.2 - - - +
302B GLY* 1.3 57.4 + - - +
304B ASN* 3.2 3.3 + - - +
305B PHE* 2.9 29.8 + - - +
488B PHE* 3.8 17.2 - - + -
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LYS 3.0 10.9 + - - -
299B LEU 3.2 2.6 + - - -
301B ASP* 1.3 76.6 - - - +
303B ALA* 1.3 61.9 + - - +
305B PHE* 3.3 1.9 + - - +
306B MET 3.1 17.3 + - - -
488B PHE* 3.2 40.8 - - - -
492B ALA* 3.2 18.0 - - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 3.7 21.1 - - - +
280B TRP* 3.5 37.9 - - + -
299B LEU 3.1 5.7 + - - -
300B LEU 3.7 4.3 - - - +
302B GLY* 1.3 77.0 - - - +
304B ASN* 1.3 51.2 + - - +
306B MET* 3.2 3.8 + - - +
307B ASP* 2.7 39.8 + - - +
491B GLY 3.5 10.7 - - - +
495B ALA* 3.8 7.4 - - + +
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Residues in contact with ASN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 3.1 27.1 - - - +
109B ASN* 4.1 2.8 - - - -
110B ARG* 3.5 16.1 + - + +
111B GLN* 2.8 43.1 - - - +
300B LEU 2.9 14.5 + - - +
301B ASP* 3.2 4.9 + - - +
303B ALA* 1.3 76.2 - - - +
305B PHE* 1.3 57.9 + - - +
307B ASP* 3.1 12.7 + - - +
308B ASN* 2.9 46.2 + - - +
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Residues in contact with PHE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.5 25.1 - - + -
48B PRO 3.2 28.0 - - - -
49B THR* 3.8 22.7 - - + -
50B PRO* 4.1 10.3 - - + -
55B ILE* 4.6 7.4 - - + -
301B ASP 2.9 15.8 + - - +
302B GLY 3.5 5.4 - - - +
303B ALA 3.2 0.2 - - - -
304B ASN* 1.3 79.0 - - - +
306B MET* 1.3 66.2 + - + +
308B ASN* 3.3 12.1 + - + +
309B HIS* 3.0 27.6 + - + +
488B PHE* 3.5 26.7 - + + -
492B ALA* 4.5 5.6 - - + -
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.4 20.2 - - + -
55B ILE* 4.8 9.9 - - + -
302B GLY 3.1 10.9 + - - +
303B ALA 3.6 6.5 - - - +
305B PHE* 1.3 79.8 - - + +
307B ASP* 1.4 65.4 + - - +
309B HIS* 3.2 26.0 + - + +
310B PHE* 2.9 22.3 + - - +
319B ALA* 5.2 0.2 - - - -
320B PRO* 4.4 4.7 - - + -
492B ALA* 3.3 40.2 - - + +
493B LEU* 5.5 0.7 - - + -
495B ALA* 3.8 6.7 - - + -
496B MET* 3.6 41.7 - - + +
499B HIS* 4.8 4.3 - - - +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.8 16.1 - - + -
105B VAL* 3.8 16.1 - - - +
108B ARG* 2.8 44.0 + - - +
303B ALA 2.7 18.5 + - - +
304B ASN* 3.1 12.0 + - - +
306B MET* 1.4 70.8 - - - +
308B ASN* 1.3 66.1 + - - +
310B PHE* 3.2 4.2 + - - +
311B CYS* 3.0 28.1 + - - -
495B ALA* 4.1 0.9 - - - +
499B HIS* 2.7 35.7 - - - -
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Residues in contact with ASN 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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89B PHE* 5.9 0.7 - - - -
111B GLN* 3.6 17.4 - - - +
304B ASN* 2.9 45.4 + - - +
305B PHE* 3.6 9.2 - - + +
307B ASP* 1.3 78.8 - - - +
309B HIS* 1.3 56.8 + - - +
311B CYS* 3.1 7.5 + - - +
312B THR* 2.9 40.8 + - + +
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.1 4.0 - - + -
47B ILE* 3.9 33.2 - - + +
305B PHE* 3.0 16.7 + - + +
306B MET* 3.2 24.4 + - + +
308B ASN* 1.3 75.3 - - - +
310B PHE* 1.3 63.9 + - - +
312B THR* 3.9 6.3 - - - -
313B ALA* 3.0 39.8 + - + +
317B LYS 3.3 22.0 - - - -
318B ASN* 3.6 2.2 - - - -
319B ALA* 3.0 26.4 + - - +
320B PRO* 3.8 19.7 - - + -
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Residues in contact with PHE 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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81B VAL* 5.0 4.7 - - + -
85B ARG* 2.9 52.9 + - + -
88B MET* 4.5 0.7 - - + -
89B PHE* 4.1 7.9 - + - -
306B MET 2.9 13.2 + - - +
307B ASP 3.2 7.4 + - - +
309B HIS* 1.3 78.0 - - - +
311B CYS* 1.3 57.7 + - - +
318B ASN* 3.0 30.2 + - - +
320B PRO* 3.6 16.4 - - + -
321B VAL* 3.9 15.7 - - + -
499B HIS* 3.2 45.1 - + + +
502B PHE* 3.8 20.0 - + - -
503B THR* 3.6 25.1 - - - -
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Residues in contact with CYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ARG* 3.5 31.4 + - - +
86B ASP* 5.3 2.7 - - - +
89B PHE* 3.5 49.8 - - - -
307B ASP 3.0 9.9 + - - +
308B ASN* 3.1 10.7 + - - +
310B PHE* 1.3 79.5 - - - +
312B THR* 1.3 64.1 + - + +
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ASN* 2.9 25.9 + - + +
309B HIS* 3.8 4.3 + - - -
311B CYS* 1.3 84.4 - - + +
313B ALA* 1.3 65.5 + - - +
314B PRO* 3.5 6.8 - - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 4.9 2.8 - - - +
85B ARG* 4.6 5.4 + - - -
309B HIS* 3.0 31.9 + - + +
310B PHE 4.5 1.0 - - - +
312B THR* 1.3 78.3 + - - +
314B PRO* 1.3 68.7 - - + +
315B LEU* 3.7 1.0 + - - +
317B LYS* 3.4 25.1 - - + +
318B ASN* 3.0 26.1 + - - +
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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