Contacts of the helix formed by residues 310 - 322 (chain A) in PDB entry 1IR1
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 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.5 23.3 - - - +
135A LEU 3.0 10.7 + - - +
136A GLU* 3.8 16.4 - - - +
302A ASP* 4.2 0.7 - - - -
309A MET* 1.3 75.7 - - - +
311A PHE* 1.3 81.2 + - + +
312A ARG* 3.0 63.8 + - - +
313A VAL* 3.1 19.3 + - - +
314A LEU* 3.7 3.9 + - - +
341A ILE* 3.5 20.5 - - + +
345A PHE* 4.2 10.8 - + - -
473A ASP* 3.0 37.6 + - - -
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TYR* 4.2 16.8 - - - -
295A ARG* 3.5 40.2 - - + +
298A HIS* 4.2 3.6 - - + -
302A ASP* 3.4 28.9 - - - +
309A MET 3.6 2.0 + - - -
310A HIS* 1.3 84.6 + - + +
312A ARG* 1.3 57.7 + - - +
314A LEU* 2.9 14.3 + - + -
315A ALA* 2.7 40.8 + - + -
326A ILE* 4.0 16.2 - - + -
327A HIS 3.4 23.6 - - - -
328A SER* 4.6 0.9 - - - -
345A PHE* 3.8 34.3 - + + -
349A LEU* 5.3 2.5 - - + -
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 2.7 67.6 + - - +
137A ASP* 3.9 19.3 - - - +
310A HIS* 3.0 42.9 + - + +
311A PHE* 1.3 76.6 - - - +
313A VAL* 1.3 58.1 + - + +
315A ALA* 3.6 2.5 - - - +
316A LYS* 3.0 33.6 + - - +
341A ILE* 4.1 15.0 + - - +
345A PHE* 3.9 30.6 - - + +
348A LEU* 4.1 14.3 - - + +
360A ARG 4.2 2.8 + - - -
361A GLY* 2.9 44.2 + - - -
362A ILE* 5.1 1.4 - - - +
363A TYR* 4.2 2.0 - - - -
475A VAL* 5.0 1.0 - - - +
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Residues in contact with VAL 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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116A MET* 6.0 0.2 - - - +
117A PHE* 3.7 14.8 - - + -
135A LEU* 3.8 22.0 - - + +
136A GLU 3.7 25.6 - - - +
137A ASP* 3.8 18.2 - - - +
138A LEU* 3.9 13.0 - - + +
309A MET* 3.7 25.8 - - + -
310A HIS 3.1 11.6 + - - +
312A ARG* 1.3 74.1 - - + +
314A LEU* 1.3 64.7 + - - +
316A LYS* 3.4 8.3 + - + +
317A ALA* 3.0 22.7 + - - +
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Residues in contact with LEU 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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117A PHE* 4.6 10.8 - - + -
269A TYR* 3.0 23.7 + - - +
270A LEU* 4.3 25.6 - - + -
274A PHE* 4.8 2.0 - - + -
298A HIS* 4.2 18.8 - - + +
301A ILE* 4.6 18.8 - - + -
302A ASP* 4.1 21.5 - - + +
309A MET* 3.9 26.5 - - + -
310A HIS 4.3 6.5 - - - +
311A PHE* 2.9 18.2 + - + +
313A VAL* 1.3 76.9 - - - +
315A ALA* 1.3 62.0 + - - +
317A ALA* 3.5 5.5 + - - +
318A LEU* 3.2 15.6 + - - +
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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
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311A PHE* 2.7 33.8 + - + +
312A ARG* 3.6 10.1 - - - +
313A VAL 3.2 0.2 - - - -
314A LEU* 1.3 75.3 - - - +
316A LYS* 1.3 65.9 + - + +
318A LEU* 3.3 4.3 + - - +
319A ARG* 3.2 16.8 + - - +
326A ILE* 4.5 9.9 - - - -
345A PHE* 4.8 6.1 - - + -
348A LEU* 6.1 1.6 - - + -
349A LEU* 3.7 34.4 - - + +
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Residues in contact with LYS 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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137A ASP* 3.0 23.5 + - - +
138A LEU* 2.7 33.2 + - + +
139A ARG* 4.7 0.2 - - - +
140A ILE* 4.6 12.6 - - + -
312A ARG 3.0 19.8 + - - +
313A VAL* 3.4 6.2 + - - +
315A ALA* 1.3 76.5 - - - +
317A ALA* 1.3 64.2 + - - +
319A ARG* 3.1 14.1 + - - +
320A LEU* 3.2 18.5 + - - +
348A LEU* 3.8 36.6 - - + +
349A LEU* 5.5 0.4 - - - -
362A ILE* 6.1 0.2 - - - +
364A PHE* 5.1 3.6 + - - +
366A GLN* 3.2 28.7 + - - +
368A TRP* 4.1 23.4 - - + -
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Residues in contact with ALA 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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113A VAL* 3.5 22.9 - - + +
116A MET* 4.8 5.6 - - + +
117A PHE* 3.5 31.2 - - + -
274A PHE* 4.0 8.3 - - + -
313A VAL 3.0 17.3 + - - +
314A LEU 3.7 6.3 - - - +
316A LYS* 1.3 77.9 - - - +
318A LEU* 1.3 56.8 + - - +
320A LEU* 3.3 6.0 + - - +
321A SER* 3.0 25.3 + - - -
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Residues in contact with LEU 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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269A TYR* 3.7 29.4 - - + -
277A ASN* 3.9 9.4 - - - +
293A ILE* 3.8 16.8 - - + -
314A LEU 3.2 11.5 + - - +
315A ALA 3.6 8.5 - - - +
316A LYS 3.2 0.8 - - - -
317A ALA* 1.3 75.3 - - - +
319A ARG* 1.3 62.1 + - - +
320A LEU 3.1 1.8 - - - -
321A SER* 4.4 2.5 - - - +
322A GLY* 2.6 47.2 + - - +
323A GLY* 4.0 21.5 - - - +
326A ILE* 3.6 36.3 - - + -
349A LEU* 5.6 0.4 - - + -
374A VAL* 4.5 7.4 - - + -
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Residues in contact with ARG 319 (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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150A GLY* 3.2 19.6 - - - -
151A PRO* 3.3 6.4 - - + +
315A ALA 3.2 11.2 + - - +
316A LYS* 3.1 10.6 + - - +
318A LEU* 1.3 77.4 - - - +
320A LEU* 1.3 60.6 + - - +
348A LEU 2.8 31.9 + - - -
349A LEU* 3.3 25.5 + - + +
350A ARG 4.0 0.6 + - - -
351A ASP 2.8 32.1 + - - -
352A ASP* 4.6 0.8 - - - +
368A TRP* 3.1 42.2 - - + +
371A THR* 2.9 30.0 + - + +
372A PRO 3.0 18.3 + - - +
373A GLY* 3.6 9.5 - - - +
374A VAL* 3.9 23.3 - - + -
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Residues in contact with LEU 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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113A VAL* 4.1 6.3 - - + -
116A MET* 4.9 7.4 - - + -
140A ILE* 4.1 30.7 - - + -
145A VAL* 4.2 22.9 - - + -
148A PHE* 3.5 55.8 - - + +
149A GLN 4.3 0.7 + - - -
150A GLY* 3.2 21.1 + - - -
316A LYS 3.2 14.3 + - - +
317A ALA* 3.6 9.2 - - - +
318A LEU 3.1 0.4 - - - -
319A ARG* 1.3 75.2 - - - +
321A SER* 1.3 66.8 + - - +
368A TRP* 3.9 20.9 - - + -
371A THR* 5.6 2.9 - - + -
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Residues in contact with SER 321 (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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113A VAL* 4.1 13.5 - - - +
148A PHE* 4.7 3.6 - - - -
149A GLN* 5.3 0.5 - - - +
150A GLY 4.0 3.1 + - - +
274A PHE* 4.1 10.9 + - - -
277A ASN* 3.0 24.7 + - - +
278A THR* 3.0 36.1 + - - +
281A SER* 3.0 17.2 + - - -
282A HIS* 5.1 2.9 + - - -
317A ALA 3.0 17.3 + - - -
318A LEU* 4.0 4.3 - - - -
320A LEU* 1.3 77.5 - - - +
322A GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 322 (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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150A GLY 3.4 17.7 - - - -
151A PRO 4.0 0.4 - - - -
152A PRO* 4.1 2.0 - - - -
277A ASN* 3.2 20.8 + - - -
281A SER* 3.4 14.3 - - - -
291A LEU* 3.7 10.2 - - - +
293A ILE* 4.2 0.3 - - - +
318A LEU* 2.6 23.3 + - - +
320A LEU 3.2 1.0 - - - -
321A SER* 1.3 75.9 - - - +
323A GLY* 1.3 57.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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