Contacts of the helix formed by residues 305 - 320 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.5 24.5 - - + -
119A SER* 3.4 15.7 + - - -
263A ARG* 3.6 32.2 - - + +
305A HIS* 6.0 3.4 + + - -
116B GLN* 5.4 1.6 + - - +
118B TYR* 3.3 42.8 - + + +
303B GLY 3.5 9.0 - - - -
304B PRO* 1.3 70.0 - - - +
306B ASN* 1.3 58.4 + - - +
307B HIS* 3.1 24.7 + + + -
308B ALA* 2.8 30.3 + - + +
309B ILE* 3.2 13.3 + - - +
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Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ARG* 5.6 0.8 - - - +
69B LEU* 3.9 15.7 + - + +
72B LYS* 3.1 29.1 + - - +
74B SER* 3.2 20.0 + - - +
89B ILE* 3.0 43.2 - - + +
92B LEU* 3.6 12.2 - - + +
93B GLU* 5.1 1.9 - - - +
304B PRO* 3.3 14.9 + - - +
305B HIS* 1.3 72.1 - - - +
307B HIS* 1.3 57.4 + - - +
309B ILE* 3.3 16.2 + - - +
310B ALA* 3.0 22.7 + - - +
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Residues in contact with HIS 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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65A LEU* 4.1 11.8 - - + +
263A ARG* 4.1 12.1 + - + +
307A HIS* 6.1 1.7 + - - -
64B ALA 4.0 8.4 - - - +
65B LEU* 3.5 47.1 - - + +
67B SER* 4.4 0.7 - - - +
69B LEU* 3.8 14.8 + - + +
70B ASN* 3.2 46.5 + - - +
305B HIS* 3.6 35.9 + + + +
306B ASN* 1.3 75.4 + - - +
308B ALA* 1.3 72.8 + - - +
310B ALA* 3.4 3.9 + - - +
311B GLY 3.2 15.8 + - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.8 14.4 - - + -
262B CYS* 3.3 10.6 - - - -
263B ARG 4.4 17.3 - - - +
264B ALA* 4.8 6.5 - - + -
305B HIS* 2.8 21.5 + - + +
307B HIS* 1.3 81.7 - - + +
309B ILE* 1.3 67.6 + - + +
311B GLY 3.0 2.4 + - - -
312B VAL* 2.9 23.1 + - - +
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Residues in contact with ILE 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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92B LEU* 4.5 12.6 - - + -
93B GLU* 4.6 15.0 - - + +
96B CYS* 3.9 27.1 - - + -
115B VAL* 3.5 38.1 - - + +
116B GLN* 4.5 5.2 - - + -
304B PRO* 4.4 16.2 - - + -
305B HIS 3.2 9.8 + - - +
306B ASN* 3.5 26.0 - - - +
308B ALA* 1.3 78.9 - - + +
310B ALA* 1.3 62.5 + - - +
312B VAL* 3.2 9.4 + - - +
313B ALA* 2.9 21.3 + - - +
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Residues in contact with ALA 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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33A VAL* 4.5 7.6 - - + +
37A ILE* 4.7 0.2 - - + -
64B ALA* 4.2 15.0 - - + -
69B LEU* 3.4 32.8 - - + -
92B LEU* 3.9 19.7 - - + +
306B ASN 3.0 6.0 + - - +
307B HIS 3.4 8.1 - - - +
309B ILE* 1.3 76.5 - - - +
311B GLY* 1.3 64.2 + - - +
313B ALA* 3.2 5.4 + - - +
314B VAL* 3.1 23.9 + - - +
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.7 19.7 - - - +
64B ALA* 4.1 12.3 - - - +
65B LEU* 5.2 1.1 - - - -
262B CYS* 3.8 16.2 - - - -
307B HIS 3.2 6.8 + - - -
308B ALA 3.0 7.5 + - - -
310B ALA* 1.3 79.7 - - - +
312B VAL* 1.3 61.9 + - - +
314B VAL* 3.2 6.9 + - - +
315B ALA* 3.0 18.4 + - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B CYS* 3.6 18.8 - - - -
115B VAL* 5.5 1.8 - - + -
255B THR* 3.7 42.0 - - + +
262B CYS* 3.8 6.5 - - - +
264B ALA* 4.1 13.5 - - + -
266B MSE 4.5 9.0 - - + -
308B ALA 2.9 17.2 + - - +
309B ILE* 3.4 10.3 - - - +
311B GLY* 1.3 75.0 - - - +
313B ALA* 1.3 55.0 + - - +
315B ALA* 2.9 8.5 + - + +
316B LEU* 2.7 46.4 + - + +
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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
----------------------------------------------------------
33A VAL* 4.0 16.4 - - + -
92B LEU* 4.7 4.7 - - + -
95B LEU* 5.1 1.6 - - + -
96B CYS* 4.0 29.2 - - + +
99B ARG* 3.0 24.3 + - - +
309B ILE 2.9 12.2 + - - +
310B ALA* 3.4 11.0 - - - +
312B VAL* 1.3 76.1 - - - +
314B VAL* 1.3 63.5 + - - +
316B LEU* 3.3 6.9 + - - +
317B LYS 3.1 13.0 + - - -
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Residues in contact with VAL 314 (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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26A LEU* 3.6 26.0 - - + -
29A SER* 4.8 0.9 - - - +
30A ASP* 3.7 16.8 - - + +
33A VAL* 3.9 13.9 - - + -
60B ALA* 3.7 33.0 - - + +
61B VAL* 3.8 11.0 - - + +
64B ALA* 4.5 4.3 - - + -
310B ALA 3.1 16.1 + - - +
311B GLY 3.4 7.4 - - - +
312B VAL 3.1 0.2 - - - -
313B ALA* 1.3 76.4 - - - +
315B ALA* 1.3 62.3 + - - +
317B LYS* 3.3 6.8 + - - +
318B GLN* 3.2 28.9 + - + +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.8 10.3 - - + -
255B THR* 5.4 1.6 - - - +
259B LEU* 4.3 13.1 - - + +
260B ARG 4.2 3.8 - - - +
261B GLY* 3.6 31.6 - - - +
311B GLY 3.0 9.7 + - - +
312B VAL* 2.9 9.9 + - + +
314B VAL* 1.3 74.6 - - - +
316B LEU* 1.3 66.1 + - - +
318B GLN* 3.2 9.8 + - - +
319B ALA* 2.8 24.1 + - - +
324B PHE* 5.9 0.2 - - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B CYS* 3.6 13.2 - - - +
99B ARG* 3.5 11.7 - - + +
100B ALA* 3.2 40.2 - - + +
103B ALA* 3.8 23.8 - - + -
104B TYR* 4.7 11.2 - - + -
259B LEU* 4.9 10.8 - - + -
266B MSE 4.8 10.8 - - + -
312B VAL* 2.7 34.6 + - + +
313B ALA* 3.5 8.7 - - - +
314B VAL 3.3 0.2 - - - -
315B ALA* 1.3 73.4 - - - +
317B LYS* 1.3 63.1 + - - +
319B ALA* 3.0 20.4 + - + +
320B MSE 3.3 14.4 + - - +
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Residues in contact with LYS 317 (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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28A ASP 5.1 0.6 + - - -
29A SER 3.0 26.6 + - - +
30A ASP* 3.6 32.0 + - + +
31A ALA 4.3 3.8 - - - +
32A GLU* 5.3 1.2 - - - +
99B ARG* 3.6 23.5 - - - +
313B ALA 3.1 3.8 + - - -
314B VAL 3.4 9.2 - - - +
315B ALA 3.2 0.2 - - - -
316B LEU* 1.3 78.8 - - - +
318B GLN* 1.3 65.7 + - + +
320B MSE 3.0 32.6 + - + +
321B THR* 3.8 9.0 - - + +
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Residues in contact with GLN 318 (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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21A MSE 4.1 32.3 + - + +
22A LEU* 4.3 6.4 - - - +
29A SER* 3.4 23.3 + - - +
58B SER* 3.1 36.1 + - - -
60B ALA* 3.4 11.5 - - - +
61B VAL* 5.0 0.7 - - - +
260B ARG* 4.8 5.6 + - - +
314B VAL* 3.2 16.4 + - - +
315B ALA* 3.2 12.9 + - - +
317B LYS* 1.3 81.3 - - + +
319B ALA* 1.3 59.7 + - - +
321B THR* 2.8 33.2 + - - -
324B PHE* 3.2 11.1 - - + +
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Residues in contact with ALA 319 (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 ALA* 5.1 2.2 - - + -
237B ALA* 4.7 15.9 - - + +
238B ALA* 5.1 1.2 - - - -
259B LEU* 4.0 16.2 - - + +
315B ALA 2.8 13.0 + - - +
316B LEU* 3.0 17.0 + - + +
318B GLN* 1.3 76.9 - - - +
320B MSE 1.3 59.2 + - + +
321B THR 3.2 2.9 + - - +
324B PHE* 2.8 48.5 - - + +
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Residues in contact with MSE 320 (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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99B ARG* 3.8 34.5 - - + +
102B GLN* 3.9 18.4 - - - +
103B ALA* 3.8 31.9 - - + -
316B LEU 3.3 21.8 - - - +
317B LYS* 3.0 27.4 + - + +
319B ALA* 1.3 74.5 - - - +
321B THR* 1.3 64.7 + - - +
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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