Contacts of the helix formed by residues 279 - 298 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 2.8 32.4 + - - +
278A GLN* 1.3 81.2 - - - +
280A PRO* 1.3 68.9 - - - +
281A GLY 3.2 3.1 - - - +
282A LEU* 3.1 19.5 + - + +
283A GLN* 3.0 19.6 + - - +
306A LEU* 3.9 16.5 - - + +
307A LYS 4.8 10.1 + - - -
309A VAL* 5.7 3.6 - - - +
320A SER* 3.9 14.8 - - - -
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Residues in contact with PRO 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.5 37.7 - - + +
54A ALA* 6.3 2.5 - - + -
55A MSE 3.7 22.9 - - + +
258A ASP 5.1 6.1 - - - +
277A GLU* 3.9 6.5 - - - +
278A GLN* 3.4 10.5 - - + +
279A ASN* 1.3 87.4 - - - +
281A GLY* 1.3 66.0 + - - +
283A GLN* 3.3 13.0 + - - +
284A ILE* 3.1 24.4 + - - +
320A SER* 4.6 5.6 - - - +
321A ARG* 5.3 13.2 - - + +
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MSE 5.7 0.2 - - - +
58A GLU* 3.8 31.3 - - - +
279A ASN 3.2 1.0 - - - -
280A PRO* 1.3 81.0 - - - +
282A LEU* 1.3 57.3 + - - +
284A ILE* 3.4 1.0 - - - +
285A ARG* 2.9 43.1 + - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASN* 3.1 27.5 + - + +
281A GLY* 1.3 76.8 - - - +
283A GLN* 1.3 60.4 + - - +
285A ARG* 4.5 6.9 - - + +
286A THR* 2.7 44.5 + - - +
289A ARG* 4.3 17.9 - - - +
306A LEU* 4.1 26.9 - - + -
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MSE 4.1 3.8 - - + +
124A VAL* 4.0 10.9 - - + +
125A ASP* 3.3 33.4 + - - +
138A VAL* 3.4 18.9 - - + +
139A GLY* 3.3 20.4 - - - +
140A ALA 3.7 5.1 + - - +
278A GLN* 2.9 47.1 + - - -
279A ASN 3.0 14.1 + - - +
280A PRO* 3.5 15.0 - - + +
282A LEU* 1.3 77.1 - - - +
284A ILE* 1.3 58.1 + - - +
287A ALA* 3.0 26.0 + - - +
306A LEU* 3.8 15.0 - - + +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.6 8.5 - - + -
44A PHE* 4.9 2.9 - - + -
55A MSE 3.6 39.9 - - + +
58A GLU* 4.1 6.7 - - + -
59A LEU* 3.7 42.8 - - + +
98A ILE* 4.2 16.4 - - + -
124A VAL* 4.2 26.9 - - + -
280A PRO 3.1 7.7 + - - +
281A GLY 3.4 10.3 - - - +
283A GLN* 1.3 75.8 - - - +
285A ARG* 1.3 68.3 + - - +
287A ALA* 3.3 1.9 + - + -
288A LEU* 3.0 22.0 + - - +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 2.7 42.4 + - - +
61A ASP* 2.7 34.5 + - - +
62A GLU* 2.8 53.9 + - + +
65A LYS* 3.9 6.6 - - - +
281A GLY* 2.9 30.2 + - - +
282A LEU* 4.0 7.2 - - - +
284A ILE* 1.3 79.5 - - + +
286A THR* 1.3 55.7 + - - +
288A LEU* 3.3 2.0 + - - +
289A ARG* 2.9 60.5 + - - +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.1 14.6 - - + -
282A LEU* 2.7 38.6 + - - +
283A GLN 3.7 3.4 - - - -
285A ARG* 1.3 74.3 - - - +
287A ALA* 1.3 66.0 + - - +
289A ARG* 3.4 11.7 + - - +
290A GLN* 3.0 43.6 + - + +
304A VAL* 4.3 16.2 - - + +
306A LEU* 5.9 2.0 - - - +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 3.8 30.2 - - + +
122A ILE* 4.5 13.9 - - + +
124A VAL* 4.6 5.4 - - + -
138A VAL* 4.3 20.5 - - + +
283A GLN 3.0 13.9 + - - +
284A ILE* 3.7 10.1 - - - +
286A THR* 1.3 78.1 - - - +
288A LEU* 1.3 57.3 + - - +
290A GLN* 3.4 2.9 + - - +
291A ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 288 (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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40A VAL* 4.1 15.9 - - + -
59A LEU* 4.0 15.7 - - + +
62A GLU* 3.9 12.1 - - + -
63A ALA* 3.6 42.0 - - + +
66A LEU* 4.0 8.1 - - + -
68A VAL* 4.0 11.7 - - + -
70A VAL* 3.9 19.7 - - + -
98A ILE* 3.8 20.8 - - + +
284A ILE 3.0 15.9 + - - +
285A ARG* 3.8 4.3 - - - +
287A ALA* 1.3 74.6 - - - +
289A ARG* 1.3 61.3 + - - +
291A ALA* 3.1 2.7 + - - +
292A VAL* 2.9 28.3 + - + +
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 2.8 42.1 + - - +
66A LEU* 4.0 15.5 - - + -
282A LEU* 4.3 21.4 - - - +
285A ARG* 2.9 35.5 + - - +
286A THR* 3.8 10.0 + - + +
288A LEU* 1.3 75.9 - - - +
290A GLN* 1.3 62.5 + - + +
292A VAL* 3.3 3.3 + - - +
293A ASP* 3.1 30.8 + - - +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.8 8.3 - - + +
138A VAL* 4.0 11.3 - - - +
286A THR* 3.0 24.4 + - + +
287A ALA 3.6 4.3 - - - +
289A ARG* 1.3 77.0 - - + +
291A ALA* 1.3 57.1 + - - +
293A ASP* 3.2 6.3 + - - +
294A LYS* 2.9 29.6 + - - +
299A ALA* 5.0 0.7 - - - +
300A ALA 4.2 2.2 - - - +
301A LEU* 3.2 19.8 - - + +
302A LYS* 2.7 51.0 + - - +
304A VAL* 3.7 19.2 - - - +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.9 17.5 - - + -
96A VAL* 3.7 29.2 - - + +
98A ILE* 4.3 7.9 - - + -
122A ILE* 5.5 0.4 - - + -
287A ALA 2.9 14.5 + - - +
288A LEU* 3.1 12.3 + - - +
290A GLN* 1.3 77.0 - - - +
292A VAL* 1.3 57.7 + - - +
294A LYS* 3.2 6.2 + - - +
295A ILE* 3.0 33.2 + - - +
301A LEU* 4.1 3.1 - - + +
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Residues in contact with VAL 292 (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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38A MSE 3.8 12.3 - - + -
40A VAL* 5.2 1.1 - - + -
66A LEU* 4.0 23.1 - - + +
68A VAL* 3.9 37.7 - - + -
288A LEU* 2.9 21.3 + - + +
289A ARG 3.8 4.5 - - - +
291A ALA* 1.3 75.5 - - + +
293A ASP* 1.3 59.8 + - - +
295A ILE* 3.2 8.0 + - - +
296A LYS* 2.9 60.3 + - + +
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Residues in contact with ASP 293 (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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289A ARG* 3.1 21.4 + - - +
290A GLN* 3.8 6.0 - - - +
292A VAL* 1.3 75.1 - - - +
294A LYS* 1.3 66.5 + - - +
296A LYS* 4.4 13.6 + - - +
297A SER* 3.0 31.8 + - - +
298A GLY 3.5 0.7 + - - -
299A ALA* 3.5 17.6 + - + -
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Residues in contact with LYS 294 (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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95A LYS 5.4 1.8 + - - -
96A VAL* 3.8 18.4 - - + -
118A GLY 6.0 0.4 + - - -
120A ALA* 3.7 23.7 - - + +
290A GLN 2.9 13.7 + - - +
291A ALA 3.2 9.8 + - - +
293A ASP* 1.3 77.0 - - - +
295A ILE* 1.3 59.1 + - - +
298A GLY* 2.9 37.2 + - - -
299A ALA 3.2 29.0 + - - +
300A ALA* 5.0 1.6 - - - +
301A LEU* 4.0 18.8 - - + +
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Residues in contact with ILE 295 (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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37A HIS* 3.6 38.6 - - + +
38A MSE 4.0 18.8 - - + -
39A GLU 3.7 20.0 - - - +
40A VAL* 3.7 16.6 - - + -
68A VAL* 4.9 2.2 - - + -
95A LYS* 5.5 6.7 - - + -
96A VAL* 3.9 17.3 - - + +
291A ALA 3.0 19.8 + - - +
292A VAL* 3.2 9.8 + - - +
294A LYS* 1.3 78.6 - - - +
296A LYS* 1.3 63.7 + - - +
298A GLY 4.7 0.2 + - - -
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MSE 4.0 23.1 - - - +
66A LEU* 5.1 6.3 + - - +
292A VAL* 2.9 44.4 + - + +
293A ASP* 4.2 13.0 + - - +
295A ILE* 1.3 76.2 - - + +
297A SER* 1.3 61.6 + - - +
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASP* 3.0 19.2 + - - +
296A LYS* 1.3 80.1 - - - +
298A GLY* 1.3 62.1 + - - +
299A ALA* 3.4 14.9 + - - +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS* 2.9 31.8 + - - +
295A ILE 4.7 0.4 + - - -
296A LYS 3.9 0.2 - - - -
297A SER* 1.3 78.3 - - - +
299A ALA* 1.3 66.7 + - - +
300A ALA* 3.4 2.6 + - - +
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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