Contacts of the helix formed by residues 305 - 320 (chain A) in PDB entry 1EJI
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 HIS 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLN* 5.4 1.4 + - - +
118A TYR* 3.4 39.0 - + + +
303A GLY 3.5 9.2 + - - -
304A PRO* 1.3 69.9 - - - +
306A ASN* 1.3 55.5 + - - +
307A HIS* 3.1 24.7 + + + -
308A ALA* 2.8 33.9 + - + +
309A ILE* 3.3 14.3 + - - +
118B TYR* 3.5 24.5 - - + -
119B SER* 3.4 19.2 + - - -
263B ARG* 3.6 34.2 + - + +
305B HIS* 6.0 3.7 + + - -
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.9 17.6 + - + +
72A LYS 3.1 26.5 + - - -
74A SER* 3.0 22.6 + - - -
89A ILE* 2.9 43.3 - - + +
92A LEU* 3.6 12.0 - - + +
93A GLU* 5.1 2.6 - - - +
304A PRO* 3.3 16.4 + - - +
305A HIS* 1.3 70.2 - - - +
307A HIS* 1.3 58.0 + - - +
309A ILE* 3.3 16.4 + - - +
310A ALA* 3.0 22.9 + - - +
263B ARG* 5.7 0.6 - - - +
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Residues in contact with HIS 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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64A ALA 4.0 8.3 - - - +
65A LEU* 3.4 47.1 - - + +
67A SER* 4.3 0.7 - - - +
69A LEU* 3.8 15.4 + - + +
70A ASN* 3.1 48.0 + - - +
305A HIS* 2.9 35.4 + + + +
306A ASN* 1.3 74.3 + - - +
308A ALA* 1.3 71.9 + - - +
310A ALA* 3.4 4.0 + - - +
311A GLY* 3.2 15.6 + - - -
65B LEU* 4.2 11.0 - - + +
262B CYS* 5.9 0.2 - - - +
263B ARG* 4.2 12.0 + - + +
307B HIS* 6.1 2.5 + - - -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.9 15.0 - - + -
262A CYS* 3.3 9.3 - - - -
263A ARG 4.4 16.6 - - - +
264A ALA* 4.8 7.4 - - + -
305A HIS* 2.8 21.9 + - + +
307A HIS* 1.3 82.2 - - + +
309A ILE* 1.3 68.6 + - + +
311A GLY 3.0 2.3 + - - -
312A VAL* 2.9 22.4 + - - +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 4.5 12.3 - - + -
93A GLU* 4.6 13.7 - - + +
96A CYS* 3.8 27.1 - - + -
115A VAL* 3.5 39.3 - - + +
116A GLN* 4.5 4.7 - - + -
304A PRO* 4.4 16.2 - - + -
305A HIS 3.3 9.8 + - - +
306A ASN* 3.5 26.7 - - - +
308A ALA* 1.3 78.4 - - + +
310A ALA* 1.3 63.1 + - - +
312A VAL* 3.2 9.5 + - - +
313A ALA* 2.9 21.5 + - - +
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Residues in contact with ALA 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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64A ALA* 4.2 13.2 - - + -
69A LEU* 3.4 33.7 - - + -
92A LEU* 3.8 19.7 - - + +
306A ASN 3.0 6.6 + - - +
307A HIS 3.5 8.1 - - - +
308A ALA 3.1 0.4 - - - -
309A ILE* 1.3 74.9 - - - +
311A GLY* 1.3 64.0 + - - +
313A ALA* 3.1 5.0 + - - +
314A VAL* 3.1 27.0 + - - +
33B VAL* 4.5 7.6 - - + +
37B ILE* 4.8 0.2 - - + -
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Residues in contact with GLY 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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61A VAL* 3.8 24.5 - - - +
64A ALA* 4.3 3.7 - - - +
65A LEU* 5.3 1.3 - - - -
262A CYS* 3.8 15.9 - - - -
307A HIS 3.2 6.5 + - - -
308A ALA 3.0 7.8 + - - -
310A ALA* 1.3 79.9 - - - +
312A VAL* 1.3 62.0 + - - +
314A VAL* 3.2 6.9 + - - +
315A ALA* 3.1 21.0 + - - +
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A CYS* 3.6 18.4 - - - -
115A VAL* 5.6 1.6 - - + -
255A THR* 3.6 40.8 - - + +
259A LEU* 6.5 0.2 - - + -
261A GLY* 5.7 0.2 - - - -
262A CYS* 3.7 6.7 - - - +
264A ALA* 4.0 14.4 - - + -
266A MSE 4.5 9.9 - - + -
308A ALA 2.9 17.4 + - - +
309A ILE* 3.5 9.6 - - - +
311A GLY* 1.3 75.7 - - - +
313A ALA* 1.3 54.2 + - - +
315A ALA* 2.9 8.4 + - + +
316A LEU* 2.7 46.1 + - + +
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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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92A LEU* 4.6 6.1 - - + -
95A LEU* 5.0 1.3 - - + -
96A CYS* 3.7 29.4 - - + +
99A ARG* 2.9 29.5 + - - +
309A ILE 2.9 12.4 + - - +
310A ALA* 3.1 11.2 + - - +
312A VAL* 1.3 75.8 - - - +
314A VAL* 1.3 61.9 + - - +
316A LEU* 3.3 6.4 + - - +
317A LYS 3.1 14.2 + - - -
33B VAL* 4.1 11.0 - - + -
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Residues in contact with VAL 314 (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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60A ALA* 3.7 33.9 - - + +
61A VAL* 3.8 10.5 - - + +
64A ALA* 4.5 2.5 - - + -
310A ALA 3.1 15.7 + - - +
311A GLY* 3.4 9.6 - - - +
312A VAL 3.1 0.2 - - - -
313A ALA* 1.3 75.9 - - - +
315A ALA* 1.3 61.6 + - - +
317A LYS* 3.3 6.2 + - - +
318A GLN* 3.2 28.6 + - + +
26B LEU* 3.6 25.8 - - + -
29B SER* 4.8 0.9 - - - +
30B ASP* 3.9 17.0 - - + +
33B VAL* 4.0 13.7 - - + -
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 3.9 10.3 - - + -
255A THR* 5.4 1.1 - - - +
259A LEU* 4.3 12.6 - - + +
260A ARG 4.2 4.5 - - - +
261A GLY* 3.7 31.9 - - - +
311A GLY 3.1 9.1 + - - +
312A VAL* 2.9 9.6 + - + +
314A VAL* 1.3 73.9 - - - +
316A LEU* 1.3 67.3 + - - +
318A GLN* 3.2 9.7 + - - +
319A ALA* 2.9 23.6 + - - +
324A PHE* 5.9 0.2 - - - -
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Residues in contact with LEU 316 (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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96A CYS* 3.6 14.4 - - - +
99A ARG* 3.4 10.8 - - + +
100A ALA* 3.2 39.5 - - + +
103A ALA* 3.8 23.5 - - + +
104A TYR* 4.7 11.2 - - + -
259A LEU* 4.8 10.8 - - + -
266A MSE 4.7 10.8 - - + -
312A VAL* 2.7 34.3 + - + +
313A ALA 3.5 8.5 - - - +
315A ALA* 1.3 72.3 - - - +
317A LYS* 1.3 64.7 + - - +
319A ALA* 3.0 20.8 + - + +
320A MSE 3.3 14.2 + - - +
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Residues in contact with LYS 317 (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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99A ARG* 3.6 24.1 - - - +
313A ALA 3.1 4.0 + - - -
314A VAL 3.5 9.0 - - - +
316A LEU* 1.3 77.4 - - - +
318A GLN* 1.3 65.7 + - + +
320A MSE 3.0 33.2 + - + +
321A THR* 3.8 8.3 + - + +
28B ASP 5.0 0.4 + - - -
29B SER 2.8 27.3 + - - +
30B ASP* 3.6 30.1 + - + +
31B ALA 4.4 3.4 - - - +
32B GLU* 5.6 0.8 - - - +
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Residues in contact with GLN 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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58A SER* 3.0 37.4 + - - -
60A ALA* 3.4 22.4 - - - +
61A VAL* 4.8 1.4 - - - +
260A ARG* 4.7 6.6 + - - +
314A VAL* 3.2 17.6 + - - +
315A ALA* 3.2 11.4 + - - +
317A LYS* 1.3 81.8 - - + +
319A ALA* 1.3 60.2 + - - +
321A THR* 2.9 32.7 + - + -
324A PHE* 3.2 10.3 - - + +
21B MSE 4.0 28.6 + - + +
22B LEU* 4.0 9.9 - - - +
29B SER* 3.6 12.0 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 5.1 2.7 - - + -
237A ALA* 4.7 15.7 - - + +
238A ALA* 5.1 1.0 - - - -
259A LEU* 4.0 15.9 - - + +
315A ALA 2.9 13.4 + - - +
316A LEU* 3.0 17.4 + - + +
318A GLN* 1.3 77.4 - - - +
320A MSE 1.3 58.9 + - - +
321A THR 3.2 2.5 + - - +
324A PHE* 2.7 49.5 - - + +
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Residues in contact with MSE 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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99A ARG* 3.8 35.2 - - + +
102A GLN* 3.9 29.8 - - - +
103A ALA* 3.8 19.3 - - + +
316A LEU 3.4 22.2 - - - +
317A LYS* 3.0 27.5 + - + +
319A ALA* 1.3 76.0 - - - +
321A THR* 1.3 63.4 + - - +
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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