Contacts of the helix formed by residues 279 - 298 (chain B) in PDB entry 4IRX
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 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B GLU* 2.8 31.9 + - - +
278B GLN* 1.3 75.0 - - - +
280B PRO* 1.3 69.3 - - - +
281B GLY 3.2 3.1 - - - +
282B LEU* 3.1 23.8 + - + +
283B GLN* 3.0 20.1 + - - +
306B LEU* 3.9 15.9 - - + -
307B LYS 5.1 6.9 - - - +
309B VAL* 6.0 1.0 - - - +
320B SER* 3.9 19.3 - - - -
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Residues in contact with PRO 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.5 38.6 - - + +
54B ALA* 6.4 1.8 - - + -
55B MSE 3.6 27.1 - - + +
258B ASP 5.2 6.3 - - - +
277B GLU* 3.9 6.5 - - - +
278B GLN* 3.4 9.8 - - + +
279B ASN* 1.3 86.8 - - - +
281B GLY* 1.3 66.2 + - - +
283B GLN* 3.5 8.6 - - + +
284B ILE* 3.0 24.8 + - - +
320B SER* 4.4 5.8 - - - +
321B ARG* 5.4 11.7 - - - +
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B MSE 5.7 0.2 - - - +
58B GLU* 3.8 34.4 - - - +
279B ASN* 3.2 1.2 - - - +
280B PRO* 1.3 83.1 - - - +
282B LEU* 1.3 56.8 + - - +
284B ILE* 3.4 1.2 + - - +
285B ARG* 3.0 40.6 + - - +
320B SER* 5.6 1.2 + - - -
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASN* 3.1 32.0 + - + +
281B GLY* 1.3 74.4 - - - +
283B GLN* 1.3 62.7 + - - +
285B ARG* 4.5 7.0 - - + +
286B THR* 2.7 45.2 + - - +
289B ARG* 4.3 17.7 - - - +
306B LEU* 4.0 26.2 - - + -
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B MSE 4.2 3.3 - - + +
124B VAL* 4.0 11.0 - - + -
125B ASP* 3.3 32.8 + - - +
138B VAL* 3.4 18.4 - - + +
139B GLY* 3.3 20.5 - - - +
140B ALA 3.7 5.9 - - - +
278B GLN* 2.9 46.1 + - - -
279B ASN 3.0 14.1 + - - +
280B PRO* 3.5 15.3 - - + +
282B LEU* 1.3 76.7 - - - +
284B ILE* 1.3 63.5 + - - +
287B ALA* 3.1 21.1 + - - +
306B LEU* 3.8 14.6 - - + -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.5 8.5 - - + -
44B PHE* 5.1 2.0 - - + -
55B MSE 3.6 40.6 - - + +
58B GLU* 4.0 6.7 - - + -
59B LEU* 3.7 43.3 - - + +
98B ILE* 4.1 27.4 - - + -
124B VAL* 4.2 17.0 - - + -
280B PRO 3.0 10.3 + - - +
281B GLY 3.5 9.4 - - - +
283B GLN* 1.3 78.8 - - - +
285B ARG* 1.3 65.9 + - - +
287B ALA* 3.4 1.8 + - + -
288B LEU* 3.0 22.6 + - - +
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 2.7 44.5 + - - +
61B ASP* 2.7 33.5 + - - +
62B GLU* 2.8 54.8 + - + +
65B LYS* 3.9 6.2 - - - +
281B GLY 3.0 23.1 + - - +
282B LEU* 4.1 7.4 - - - +
284B ILE* 1.3 79.5 - - + +
286B THR* 1.3 55.4 + - - +
288B LEU* 3.3 2.5 + - - +
289B ARG* 2.8 60.4 + - - +
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.1 11.2 - - + -
282B LEU* 2.7 38.1 + - - +
283B GLN 3.7 2.9 - - - -
285B ARG* 1.3 73.6 - - - +
287B ALA* 1.3 64.9 + - - +
289B ARG* 3.3 11.8 + - - +
290B GLN* 3.0 43.6 + - + +
304B VAL* 4.1 20.9 - - + +
306B LEU* 5.7 2.2 - - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 3.8 31.0 - - + +
122B ILE* 4.5 14.3 - - + +
124B VAL* 4.6 4.9 - - + -
138B VAL* 4.2 20.8 - - + +
283B GLN 3.1 16.7 + - - +
284B ILE* 3.7 7.0 - - - +
286B THR* 1.3 76.8 - - - +
288B LEU* 1.3 57.0 + - - +
290B GLN* 3.4 3.1 + - - +
291B ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.2 15.5 - - + -
59B LEU* 4.0 16.6 - - + +
62B GLU* 3.9 8.7 - - + -
63B ALA* 3.6 40.4 - - + +
66B LEU* 4.0 13.0 - - + -
68B VAL* 4.0 11.0 - - + -
70B VAL* 4.0 19.7 - - + -
98B ILE* 3.8 20.1 - - + +
284B ILE 3.0 16.5 + - - +
285B ARG* 3.8 5.2 - - - +
287B ALA* 1.3 74.8 - - - +
289B ARG* 1.3 60.0 + - - +
291B ALA* 3.1 3.0 + - - +
292B VAL* 3.0 28.6 + - + +
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 2.8 41.9 + - - +
66B LEU* 4.1 16.4 - - + -
282B LEU* 4.3 20.6 - - - +
285B ARG* 2.8 40.4 + - - +
286B THR* 3.7 9.8 + - - +
288B LEU* 1.3 76.0 - - - +
290B GLN* 1.3 62.1 + - + +
292B VAL* 3.3 3.2 + - - +
293B ASP* 3.1 31.1 + - - +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.6 10.9 - - + +
138B VAL* 4.1 4.9 - - - +
286B THR* 3.0 27.9 + - + +
287B ALA 3.6 5.4 - - - +
289B ARG* 1.3 75.2 - - + +
291B ALA* 1.3 64.6 + - - +
293B ASP* 3.2 6.9 + - - +
294B LYS* 2.9 23.6 + - - +
299B ALA* 5.0 0.7 - - - +
300B ALA 4.3 1.2 - - - +
301B LEU* 3.3 19.6 - - + +
302B LYS* 2.7 51.9 + - - +
304B VAL* 3.7 19.2 - - - +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.9 22.4 - - + -
96B VAL* 3.7 28.8 - - + +
98B ILE* 4.4 2.9 - - + -
122B ILE* 5.6 0.7 - - + -
287B ALA 3.0 15.1 + - - +
288B LEU* 3.1 13.2 + - - +
290B GLN* 1.3 75.6 - - - +
292B VAL* 1.3 57.9 + - - +
294B LYS* 3.2 4.2 + - - +
295B ILE* 3.0 33.6 + - - +
301B LEU* 4.1 4.9 - - - +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MSE 3.9 12.6 - - + -
40B VAL* 5.2 1.1 - - + -
66B LEU* 3.8 29.2 - - + +
68B VAL* 4.0 31.0 - - + -
288B LEU* 3.0 21.0 + - + +
289B ARG 3.8 4.7 - - - +
291B ALA* 1.3 76.2 - - + +
293B ASP* 1.3 59.2 + - - +
295B ILE* 3.2 8.0 + - + +
296B LYS* 2.9 60.0 + - + +
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ARG* 3.1 21.9 + - - +
290B GLN* 3.2 6.2 + - - +
292B VAL* 1.3 75.7 - - - +
294B LYS* 1.3 66.6 + - - +
296B LYS* 4.4 14.0 + - - +
297B SER* 3.0 32.3 + - - +
298B GLY 3.5 0.3 + - - -
299B ALA* 3.5 17.6 + - + -
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Residues in contact with LYS 294 (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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95B LYS* 5.3 2.6 + - - +
96B VAL* 3.9 18.2 - - + -
118B GLY 5.9 1.2 + - - -
120B ALA* 3.8 24.5 - - + +
290B GLN 2.9 13.0 + - - +
291B ALA 3.2 9.6 + - - +
293B ASP* 1.3 77.4 - - - +
295B ILE* 1.3 59.4 + - - +
298B GLY* 2.9 36.8 + - - +
299B ALA 3.2 28.3 + - - +
300B ALA* 5.0 1.8 - - - +
301B LEU* 4.0 16.6 - - + +
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.5 39.5 - - + +
38B MSE 4.0 18.6 - - + -
39B GLU 3.7 18.8 - - - +
40B VAL* 3.7 17.5 - - + -
68B VAL* 4.9 2.5 - - + -
95B LYS* 5.5 7.2 - - + -
96B VAL* 3.8 17.3 - - + +
291B ALA 3.0 19.8 + - - +
292B VAL* 3.2 9.6 + - - +
294B LYS* 1.3 78.3 - - - +
296B LYS* 1.3 64.3 + - - +
298B GLY 4.7 0.2 + - - -
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Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MSE 4.0 22.6 - - - +
66B LEU* 5.1 5.5 + - - +
292B VAL* 2.9 42.5 + - + +
293B ASP* 4.2 13.2 + - - +
295B ILE* 1.3 80.9 - - + +
297B SER* 1.3 61.7 + - - +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ASP* 3.0 17.8 + - - +
296B LYS* 1.3 80.3 - - - +
298B GLY* 1.3 61.6 + - - +
299B ALA* 3.4 14.6 + - - +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS* 2.9 31.0 + - - +
295B ILE 4.7 0.4 + - - -
296B LYS 3.9 0.2 - - - -
297B SER* 1.3 78.5 - - - +
299B ALA* 1.3 67.0 + - - +
300B ALA* 3.4 2.9 + - - +
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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
------------------------------------------------------------
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