Contacts of the helix formed by residues 292 - 313 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 4.2 13.5 - - - -
180A ASN* 4.1 4.1 - - - +
288A SER 2.9 18.0 + - - +
290A TYR 3.6 1.6 - - - -
291A ILE* 1.3 82.3 - - - +
293A PHE* 1.3 65.6 + - - -
294A GLU* 3.3 5.6 - - - -
295A ASN 3.2 2.0 + - - -
296A PHE* 3.1 18.9 + - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 6.3 0.2 - - - -
130A LEU* 3.4 46.0 - - + -
133A MET* 4.2 7.0 - - + -
134A LYS* 3.5 50.7 - - + +
137A SER* 4.6 7.1 - - - -
138A THR* 6.0 2.2 - - + -
141A ILE* 5.2 0.4 - - - +
288A SER* 3.4 24.3 + - - +
292A GLY* 1.3 72.4 - - - -
294A GLU* 1.4 53.8 + - - +
296A PHE* 3.1 20.0 + + - +
297A GLU* 2.7 71.8 + - + +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE 5.4 0.7 - - - +
292A GLY* 3.3 3.1 - - - +
293A PHE* 1.4 78.0 - - - +
295A ASN* 1.3 75.3 + - - +
297A GLU* 3.4 18.9 + - - +
298A LYS* 3.1 40.5 + - - +
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Residues in contact with ASN 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 3.8 28.8 + - - +
291A ILE* 2.9 42.9 + - + +
292A GLY 3.2 1.7 + - - +
293A PHE 3.2 0.4 - - - -
294A GLU* 1.3 93.8 + - - +
296A PHE* 1.3 64.2 + - - +
298A LYS* 3.2 22.7 + - - +
299A LEU* 3.1 19.4 + - - +
487A PRO* 3.4 23.5 - - + +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.0 10.1 - - + -
133A MET* 3.8 17.5 - - + -
279A LEU 3.6 25.4 - - - -
280A TRP* 3.7 14.8 - - - -
281A SER 3.9 7.9 - - - -
284A GLY* 3.9 11.0 - - - -
287A ILE* 3.8 24.7 - - + -
288A SER* 4.0 17.3 - - - +
291A ILE* 4.3 4.8 - - - +
292A GLY 3.1 12.7 + - - +
293A PHE* 3.4 25.4 - + - +
295A ASN* 1.3 74.7 - - - +
297A GLU* 1.3 64.5 + - - +
299A LEU* 3.1 23.3 + - + +
300A LEU* 3.0 41.9 + - + +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.2 27.8 + - - +
134A LYS* 4.9 5.7 + - - -
293A PHE* 2.7 57.0 + - + +
294A GLU* 3.5 19.0 - - - +
295A ASN 3.2 0.2 - - - -
296A PHE* 1.3 73.3 - - - +
298A LYS* 1.3 56.2 + - + +
300A LEU* 3.1 14.6 + - + +
301A ASP* 2.9 33.7 + - - +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 3.1 25.3 + - - +
295A ASN* 3.2 27.0 + - - +
297A GLU* 1.3 77.3 - - + +
299A LEU* 1.3 58.0 + - - +
301A ASP* 3.5 13.6 - - - +
302A GLY 3.0 22.9 + - - -
487A PRO* 3.8 13.7 - - + -
488A PHE* 3.4 20.8 - - + +
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Residues in contact with LEU 299 (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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171A VAL* 4.2 17.3 - - + -
175A LEU* 4.6 4.3 - - + -
279A LEU* 3.8 26.0 - - + -
280A TRP* 3.8 12.2 - - + -
287A ILE* 4.5 2.5 - - + -
291A ILE* 5.9 0.2 - - + -
295A ASN 3.1 13.1 + - - +
296A PHE* 3.1 30.5 + - + +
298A LYS* 1.3 76.7 - - - +
300A LEU* 1.4 61.4 + - + +
302A GLY 3.2 1.9 + - - -
303A ALA 3.1 18.0 + - - -
487A PRO* 3.3 23.9 - - + +
490A LEU* 4.3 18.4 - - + -
491A GLY* 3.6 26.0 - - - +
494A ILE* 4.6 5.2 - - + -
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Residues in contact with LEU 300 (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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107A LEU 4.1 5.2 - - - +
108A ARG* 3.5 17.0 - - + +
110A ARG* 4.0 30.1 - - - +
130A LEU* 3.9 30.3 - - + -
280A TRP* 3.7 44.2 - - + +
296A PHE* 3.0 31.9 + - + +
297A GLU* 3.5 12.8 - - + +
299A LEU* 1.4 76.0 - - + +
301A ASP* 1.4 57.5 + - - +
303A ALA* 3.2 3.8 + - - +
304A ASN* 2.8 29.6 + - - +
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Residues in contact with ASP 301 (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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110A ARG* 2.8 38.5 + - - +
297A GLU* 2.9 19.0 + - - +
298A LYS* 3.5 18.9 + - - +
299A LEU 3.3 0.2 - - - -
300A LEU* 1.4 76.2 - - - +
302A GLY* 1.3 57.9 + - - +
304A ASN* 3.3 3.3 + - - +
305A PHE* 2.8 30.1 + - - +
488A PHE* 3.7 16.8 - - + -
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Residues in contact with GLY 302 (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 LYS 3.0 10.9 + - - -
299A LEU 3.2 2.6 + - - -
301A ASP* 1.3 77.6 - - - +
303A ALA* 1.3 61.9 + - - +
305A PHE* 3.2 4.5 + - - +
306A MET 3.1 17.5 + - - -
488A PHE* 3.3 40.1 - - - -
492A ALA* 3.3 16.3 - - - -
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Residues in contact with ALA 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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108A ARG* 3.7 20.2 - - - +
280A TRP* 3.5 37.0 - - + -
299A LEU 3.1 5.5 + - - -
300A LEU 3.2 7.2 + - - +
302A GLY* 1.3 75.5 - - - +
304A ASN* 1.3 57.3 + - - +
306A MET* 3.1 4.3 + - - +
307A ASP* 2.9 32.6 + - - +
491A GLY 3.5 10.7 - - - +
495A ALA* 3.8 6.9 - - + +
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL 5.6 0.2 - - - +
108A ARG* 3.1 26.2 - - - +
109A ASN* 4.1 1.7 - - - -
110A ARG* 3.6 16.5 + - + +
111A GLN* 2.8 44.3 + - - +
300A LEU 2.8 16.2 + - - +
301A ASP 3.5 5.5 + - - +
303A ALA* 1.3 71.8 - - - +
305A PHE* 1.3 64.7 + - - +
307A ASP* 3.1 13.5 + - - +
308A ASN* 3.0 32.7 + - - +
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Residues in contact with PHE 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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47A ILE* 3.7 26.0 - - + -
48A PRO 3.3 26.9 - - - -
49A THR* 3.8 14.1 - - + -
50A PRO* 4.2 16.6 - - + -
55A ILE* 4.5 7.6 - - + -
301A ASP 2.8 15.1 + - - +
302A GLY 3.3 9.9 - - - +
304A ASN* 1.3 79.3 - - - +
306A MET* 1.4 65.6 + - + +
308A ASN* 3.4 11.6 + - + +
309A HIS* 3.1 26.6 + - + +
488A PHE* 3.5 26.9 - + + -
492A ALA* 4.4 7.0 - - + -
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Residues in contact with MET 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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47A ILE* 4.4 19.5 - - + -
55A ILE* 4.8 11.2 - - + -
302A GLY 3.1 10.9 + - - +
303A ALA 3.1 7.2 + - - +
305A PHE* 1.4 80.3 - - + +
307A ASP* 1.3 61.1 + - - +
309A HIS* 3.3 23.9 + - + +
310A PHE* 2.9 28.5 + - - +
319A ALA* 5.1 0.2 - - - -
320A PRO* 4.4 4.7 - - - -
492A ALA* 3.3 40.6 - - + +
493A LEU* 5.6 0.7 - - + -
495A ALA* 3.9 6.7 - - + +
496A MET* 3.4 42.0 - - + +
499A HIS* 4.7 3.1 - - + -
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Residues in contact with ASP 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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89A PHE* 3.8 18.7 - - + -
105A VAL* 3.9 14.5 - - - +
108A ARG* 2.8 46.7 + - - +
303A ALA 2.9 15.0 + - - +
304A ASN* 3.5 11.8 - - - +
306A MET* 1.3 77.8 - - - +
308A ASN* 1.3 60.1 + - - +
310A PHE* 3.3 4.2 + - - +
311A CYS* 3.1 28.6 + - - +
495A ALA* 4.1 0.9 - - - +
499A HIS* 2.7 34.5 + - - -
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Residues in contact with ASN 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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89A PHE* 5.8 1.4 - - - -
111A GLN* 3.3 31.7 + - - +
304A ASN* 3.0 26.5 + - - +
305A PHE* 3.5 11.3 - - + +
306A MET 3.2 0.2 - - - -
307A ASP* 1.3 75.9 - - - +
309A HIS* 1.3 63.1 + - - +
311A CYS* 3.2 6.1 + - - +
312A THR* 2.8 38.8 + - + +
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Residues in contact with HIS 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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45A LEU* 4.2 3.8 - - + -
47A ILE* 3.9 33.7 - - + +
305A PHE* 3.1 16.5 + - + +
306A MET* 3.3 31.6 + - + +
308A ASN* 1.3 75.6 - - - +
310A PHE* 1.3 65.1 + - - +
312A THR* 3.8 5.2 - - - -
313A ALA* 3.0 41.4 + - + +
317A LYS 3.3 22.7 - - - -
318A ASN* 3.8 1.4 - - - -
319A ALA* 3.0 26.7 + - + +
320A PRO* 3.8 11.0 - - + -
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Residues in contact with PHE 310 (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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81A VAL* 5.1 4.0 - - + -
85A ARG* 2.9 53.7 + - + -
88A MET* 4.6 0.9 - - + -
89A PHE* 3.9 7.2 - + - -
306A MET 2.9 17.4 + - - +
307A ASP 3.3 4.2 + - - +
309A HIS* 1.3 77.4 - - - +
311A CYS* 1.3 57.8 + - - +
318A ASN* 2.9 31.4 + - - +
320A PRO* 4.0 12.6 - - + -
321A VAL* 4.0 16.6 - - + -
499A HIS* 3.3 46.4 - + + -
502A PHE* 3.8 20.4 - + - -
503A THR* 3.5 24.9 - - - -
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Residues in contact with CYS 311 (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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85A ARG* 3.4 36.5 + - - +
86A ASP* 4.8 6.7 - - - -
89A PHE* 4.9 19.1 - - + -
307A ASP 3.1 16.2 + - - +
308A ASN* 3.6 7.4 - - - +
309A HIS 3.2 0.2 - - - -
310A PHE* 1.3 78.7 - - - +
312A THR* 1.3 67.0 + - + +
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Residues in contact with THR 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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308A ASN* 2.8 36.6 + - + +
309A HIS* 3.7 4.3 + - - -
311A CYS* 1.3 85.8 - - + +
313A ALA* 1.3 65.2 + - - +
314A PRO* 3.6 4.5 - - - +
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Residues in contact with ALA 313 (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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82A GLU* 5.0 2.4 - - - +
85A ARG* 4.6 5.5 + - - -
309A HIS* 3.0 32.7 + - + +
310A PHE 4.4 1.2 - - - +
312A THR* 1.3 78.9 + - - +
314A PRO* 1.3 71.4 - - + +
315A LEU* 3.7 0.3 + - - +
317A LYS* 3.4 25.1 - - + +
318A ASN* 3.1 21.9 + - - -
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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