Contacts of the helix formed by residues 312 - 328 (chain A) in PDB entry 1JX6
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 ASN 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASP* 5.3 0.9 - - - +
81A TYR* 3.4 33.8 - - - -
84A ARG* 3.3 34.8 - - - +
85A ASN* 4.3 3.6 + - - +
88A SER* 5.1 0.2 + - - -
178A PHE* 3.5 10.5 - - - -
310A ARG* 2.7 18.2 + - + +
311A MET* 1.3 70.1 - - - +
313A ASP* 1.3 84.9 + - - +
314A ASP 3.0 1.6 + - - -
315A THR* 3.2 21.1 + - - -
316A GLY 4.4 0.5 + - - -
359A ALA* 3.5 9.7 - - - +
360A PHE* 3.9 16.1 - - + -
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 3.6 23.7 + - - -
311A MET 3.2 0.6 + - - -
312A ASN* 1.3 90.7 + - - +
314A ASP* 1.3 63.1 + - - +
315A THR 3.2 0.4 - - - -
316A GLY 3.1 2.9 + - - -
317A ILE* 3.0 27.1 + - + +
358A ARG 5.2 0.4 - - - +
359A ALA 2.9 20.5 + - - +
360A PHE 3.1 4.0 - - - -
361A ARG* 4.4 14.6 - - + +
362A TYR* 2.7 31.3 + - + -
363A SER* 2.7 32.1 + - - -
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.9 16.9 - - + +
53A ARG* 4.6 4.4 - - - -
178A PHE* 4.5 6.7 - - + -
311A MET* 3.1 19.8 + - - +
312A ASN 3.0 1.0 + - - -
313A ASP* 1.3 76.6 - - - +
315A THR* 1.3 58.1 + - - +
317A ILE* 3.5 2.8 + - - +
318A ALA* 2.9 28.8 + - - +
336A TYR* 3.6 18.7 + - + +
338A GLY* 4.9 1.3 - - - -
339A ASP* 5.1 4.9 + - - +
358A ARG* 2.9 32.6 + - - +
361A ARG* 2.8 26.9 + - - -
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Residues in contact with THR 315 (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 TYR* 3.1 19.2 + - - -
85A ASN* 3.3 10.1 + - - -
158A GLN* 4.0 0.7 - - - -
176A VAL* 3.7 17.7 - - + -
177A GLY* 3.4 32.5 - - - +
178A PHE* 3.3 22.6 - - + -
312A ASN 3.2 13.7 + - - -
313A ASP 3.1 0.2 + - - -
314A ASP* 1.3 75.1 - - - +
316A GLY* 1.3 65.7 + - - +
318A ALA* 3.2 4.0 + - - +
319A MET* 3.0 27.5 + - - +
336A TYR* 4.1 8.1 - - + -
338A GLY 4.5 0.2 - - - +
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 3.4 21.5 - - - +
88A SER* 3.3 18.6 + - - -
89A PHE* 3.4 21.6 - - - -
312A ASN 4.4 0.2 + - - -
313A ASP 3.1 4.8 + - - -
315A THR* 1.3 80.8 + - - +
317A ILE* 1.3 61.1 + - - +
319A MET* 3.3 13.8 + - - +
320A ALA* 3.3 8.8 + - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.9 22.4 - - + +
88A SER* 4.3 2.7 + - - +
92A ARG* 3.5 36.3 - - + +
313A ASP* 3.0 21.0 + - + +
314A ASP 3.7 3.4 - - - +
316A GLY* 1.3 74.5 - - - +
318A ALA* 1.3 64.4 + - - +
320A ALA* 3.2 4.3 + - - +
321A GLU* 3.0 22.3 + - + +
361A ARG* 3.3 39.7 - - - +
362A TYR* 4.0 39.5 - - + -
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Residues in contact with ALA 318 (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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48A LEU* 3.9 12.2 - - + +
52A VAL* 3.6 17.0 - - + -
174A LEU* 5.0 1.3 - - + -
176A VAL* 4.5 4.0 - - + -
314A ASP 2.9 18.1 + - - +
315A THR 3.2 5.6 + - - +
317A ILE* 1.3 75.9 - - - +
319A MET* 1.3 58.7 + - - +
321A GLU* 3.3 1.9 + - - +
322A ALA* 2.9 30.3 + - - +
336A TYR* 3.6 33.0 - - + -
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Residues in contact with MET 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 3.7 3.1 - - - +
85A ASN* 3.7 13.9 - - - +
86A ILE* 6.2 0.2 - - + -
89A PHE* 3.6 16.2 - - + -
132A ILE* 3.6 28.0 - - + -
156A ILE* 3.4 29.8 - - + +
158A GLN* 3.1 31.2 - - - +
174A LEU* 4.4 4.7 - - + -
176A VAL* 4.0 14.8 - - + -
315A THR 3.0 15.4 + - - +
316A GLY* 3.5 8.3 - - - +
317A ILE 3.2 0.2 - - - -
318A ALA* 1.3 75.8 - - - +
320A ALA* 1.3 64.5 + - - +
322A ALA* 3.5 5.8 + - - +
323A ILE* 3.1 28.8 + - - +
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Residues in contact with ALA 320 (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* 3.6 15.2 - - + +
92A ARG* 3.5 36.6 - - + -
93A LEU* 3.9 23.6 - - + +
96A LEU* 3.7 7.3 - - + +
98A ILE* 4.1 2.9 - - - +
316A GLY 3.3 2.2 + - - +
317A ILE 3.2 2.7 + - - +
319A MET* 1.3 78.5 - - - +
321A GLU* 1.3 58.6 + - - +
323A ILE* 3.4 3.5 + - - +
324A LYS* 3.0 26.7 + - - +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 17.7 - - + -
51A ALA* 4.1 22.1 - - + +
52A VAL* 4.8 0.2 - - + -
56A PRO* 4.8 1.0 - - - +
57A VAL 4.9 0.5 + - - -
92A ARG* 2.9 36.7 + - - +
96A LEU* 3.6 16.1 - - - +
317A ILE* 3.0 26.4 + - + +
318A ALA 3.7 4.3 - - - +
319A MET 3.3 0.2 - - - -
320A ALA* 1.3 74.6 - - - +
322A ALA* 1.3 59.6 + - - +
324A LYS* 2.9 34.9 + - - +
325A TRP* 2.9 37.0 + - + -
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.8 6.0 - - + +
173A PHE* 3.5 11.4 - - + -
174A LEU* 3.9 19.1 - - + -
318A ALA 2.9 18.5 + - - +
319A MET 3.7 4.7 - - - +
321A GLU* 1.3 77.0 - - - +
323A ILE* 1.3 61.0 + - - +
325A TRP* 3.3 5.5 + - - -
326A ASP 3.0 18.4 + - - -
332A VAL* 3.5 35.4 - - + +
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.8 23.1 - - + -
69A ILE* 4.3 9.4 - - + -
89A PHE* 3.7 30.7 - - + -
93A LEU* 4.7 2.7 - - + -
98A ILE* 4.5 6.1 - - + -
130A TYR* 3.9 43.5 - - + -
132A ILE* 5.3 0.2 - - + -
156A ILE* 4.3 12.3 - - + -
173A PHE* 4.5 2.9 - - + -
319A MET 3.1 14.2 + - - +
320A ALA* 3.7 4.9 - - - +
321A GLU 3.3 0.2 - - - -
322A ALA* 1.3 76.7 - - - +
324A LYS* 1.3 64.4 + - - +
326A ASP* 3.2 7.4 + - - +
327A LEU* 2.9 31.7 + - + +
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Residues in contact with LYS 324 (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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51A ALA* 5.8 1.8 - - - +
57A VAL* 2.8 41.1 + - - +
59A LEU* 4.0 21.1 - - + +
96A LEU* 3.9 12.3 - - + +
98A ILE* 4.0 14.8 - - + +
320A ALA 3.0 15.1 + - - +
321A GLU* 2.9 34.1 + - - +
323A ILE* 1.3 77.6 - - - +
325A TRP* 1.3 84.8 + - - +
327A LEU* 3.1 7.7 + - - +
328A GLU* 3.0 45.4 + - - +
330A LYS* 5.9 0.4 - - - +
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Residues in contact with TRP 325 (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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44A LEU* 4.2 6.1 - - + -
47A ALA* 3.5 20.9 - - + -
48A LEU* 3.4 38.1 - - + -
51A ALA* 4.0 16.0 - - + +
321A GLU* 2.9 21.4 + - + -
322A ALA* 3.7 8.7 - - - +
323A ILE 3.3 0.2 - - - -
324A LYS* 1.3 93.0 - - - +
326A ASP* 1.3 60.8 + - - +
328A GLU* 3.0 19.9 + - - -
329A ASP 3.0 4.7 + - - -
330A LYS* 2.8 51.8 + - + +
331A PRO 3.5 17.9 - - - -
332A VAL* 3.8 10.5 - - + -
333A PRO* 3.9 24.9 - - + -
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Residues in contact with ASP 326 (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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130A TYR* 2.7 21.2 + - - +
154A LYS* 2.9 42.6 + - - +
173A PHE* 3.6 19.9 - - + -
322A ALA 3.0 14.3 + - - +
323A ILE 3.2 8.7 + - - +
325A TRP* 1.3 75.6 - - - +
327A LEU* 1.3 58.1 + - - +
329A ASP* 3.0 24.6 + - - +
330A LYS 4.4 8.2 - - - +
332A VAL* 4.0 1.0 - - - +
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Residues in contact with LEU 327 (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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59A LEU* 3.8 19.3 - - + -
61A LYS* 4.4 14.6 - - - +
63A THR* 3.7 31.7 - - + +
67A ILE* 4.0 15.9 - - + -
98A ILE* 4.1 23.3 - - + -
130A TYR* 3.7 17.3 - - + +
323A ILE* 2.9 31.4 + - + +
324A LYS 3.1 6.9 + - - +
326A ASP* 1.3 76.9 - - - +
328A GLU* 1.3 58.4 + - - +
329A ASP* 3.2 6.7 + - - +
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 4.2 2.1 - - - +
59A LEU* 3.7 17.1 - - + -
60A SER* 2.9 44.4 + - - +
61A LYS* 4.6 19.6 + - + +
324A LYS* 3.0 31.8 + - - +
325A TRP* 3.0 14.3 + - - +
327A LEU* 1.3 75.6 - - - +
329A ASP* 1.3 69.6 + - - +
330A LYS* 3.2 43.2 + - + +
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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