Contacts of the helix formed by residues 310 - 322 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG* 3.4 37.0 - - - +
135B LEU 3.0 10.8 + - - +
136B GLU* 3.8 16.4 - - - +
302B ASP* 4.1 0.4 - - - -
309B MET* 1.3 76.6 - - - +
311B PHE* 1.3 81.4 + - + +
312B ARG* 3.1 59.9 + - - +
313B VAL* 3.1 17.5 + - - +
314B LEU* 3.6 5.4 + - - +
341B ILE* 3.5 22.5 - - + +
345B PHE* 4.2 10.8 - + - -
473B ASP* 3.0 25.5 + - - -
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR* 4.2 15.5 - - - -
295B ARG* 3.5 41.5 - - + +
298B HIS* 4.1 4.0 - - + +
302B ASP* 3.4 30.6 - - - +
310B HIS* 1.3 82.8 + - + +
312B ARG* 1.3 60.8 + - - +
314B LEU* 2.8 14.1 + - + +
315B ALA* 2.7 41.5 + - + +
326B ILE* 3.9 16.6 - - + -
327B HIS 3.4 22.9 - - - -
328B SER* 4.6 0.7 - - - -
345B PHE* 3.8 34.5 - + + -
349B LEU* 5.1 3.1 - - + -
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLU* 2.8 64.8 + - - +
137B ASP* 4.0 17.9 - - - +
310B HIS* 3.1 39.9 + - - +
311B PHE* 1.3 77.4 - - - +
313B VAL* 1.3 60.6 + - + +
315B ALA* 3.5 3.0 - - - +
316B LYS* 3.1 33.4 + - - +
341B ILE* 4.1 12.1 + - - +
344B GLY 6.2 0.2 - - - -
345B PHE* 3.8 31.2 - - + +
348B LEU* 4.2 14.9 - - + +
360B ARG 4.1 6.1 + - - -
361B GLY* 2.8 43.2 + - - -
362B ILE* 5.0 1.9 - - - +
363B TYR* 4.4 1.0 - - - -
475B VAL* 6.1 1.0 - - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.7 26.5 - - + -
135B LEU* 3.9 19.3 - - + +
136B GLU 3.5 27.4 - - - +
137B ASP* 3.7 20.6 - - - +
138B LEU* 3.9 12.6 - - + +
309B MET* 3.8 13.7 - - + -
310B HIS 3.1 11.4 + - - +
311B PHE 3.0 0.6 - - - -
312B ARG* 1.3 75.9 - - + +
314B LEU* 1.3 65.0 + - - +
316B LYS* 3.5 7.8 + - - +
317B ALA* 3.2 21.8 + - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 4.6 10.3 - - + -
269B TYR* 3.1 25.9 + - - +
270B LEU* 4.3 24.0 - - + -
274B PHE* 4.8 3.1 - - + -
298B HIS* 4.2 21.8 - - + +
301B ILE* 4.6 18.6 - - + -
302B ASP* 4.0 21.1 - - + +
309B MET* 4.2 26.0 - - + -
310B HIS 4.2 7.9 - - - +
311B PHE* 2.8 14.4 + - + +
313B VAL* 1.3 76.9 - - - +
315B ALA* 1.3 60.7 + - - +
317B ALA* 3.5 5.9 + - - +
318B LEU* 3.2 15.6 + - - +
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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
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311B PHE* 2.7 32.4 + - + +
312B ARG* 3.5 10.3 - - - +
314B LEU* 1.3 75.3 - - - +
316B LYS* 1.3 66.0 + - + +
318B LEU* 3.2 4.7 + - - +
319B ARG* 3.1 17.3 + - - +
326B ILE* 4.6 9.4 - - - -
345B PHE* 4.8 5.6 - - + +
348B LEU* 6.1 1.6 - - + -
349B LEU* 3.7 34.2 - - + +
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Residues in contact with LYS 316 (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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137B ASP* 3.1 22.1 + - - +
138B LEU* 2.6 35.3 + - + +
139B ARG* 4.7 0.8 - - - +
140B ILE* 4.0 18.8 - - + -
312B ARG 3.1 20.3 + - - +
313B VAL* 3.5 7.2 + - + +
314B LEU 3.5 0.2 - - - -
315B ALA* 1.3 76.3 - - - +
317B ALA* 1.3 61.9 + - - +
319B ARG* 3.2 4.8 + - - +
320B LEU* 3.2 28.8 + - - +
348B LEU* 3.8 36.9 - - + +
349B LEU* 5.6 0.2 - - - -
362B ILE* 6.2 0.2 - - - +
364B PHE* 5.0 4.0 + - - +
366B GLN* 3.1 29.4 + - - +
368B TRP* 4.0 20.6 - - + -
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Residues in contact with ALA 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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113B VAL* 3.6 20.6 - - + +
116B MET* 4.8 4.2 - - + +
117B PHE* 3.6 29.4 - - + -
274B PHE* 4.0 8.3 - - + -
313B VAL 3.2 17.4 + - - +
314B LEU 3.6 7.0 - - - +
315B ALA 3.2 0.2 - - - -
316B LYS* 1.3 77.8 - - - +
318B LEU* 1.3 56.6 + - - +
320B LEU* 3.4 5.6 + - - -
321B SER* 3.0 29.1 + - - -
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR* 3.7 28.5 - - + -
277B ASN* 3.9 11.2 - - - +
293B ILE* 3.9 16.6 - - + -
314B LEU 3.2 12.8 + - - +
315B ALA 3.2 8.0 + - - +
317B ALA* 1.3 75.2 - - - +
319B ARG* 1.3 61.5 + - - +
321B SER* 4.5 1.6 - - - +
322B GLY* 2.7 46.6 + - - +
323B GLY* 4.0 22.4 - - - +
326B ILE* 3.7 35.2 - - + -
349B LEU* 5.5 0.7 - - + -
374B VAL* 4.4 8.1 - - + -
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLY* 3.2 23.2 - - - -
151B PRO* 3.3 6.7 - - + +
315B ALA 3.1 12.2 + - - +
316B LYS* 3.2 8.7 + - - +
318B LEU* 1.3 76.3 - - - +
320B LEU* 1.3 58.5 + - - +
348B LEU 2.8 32.3 + - - -
349B LEU* 3.3 26.1 + - + +
350B ARG 3.9 2.2 + - - -
351B ASP 2.9 30.5 + - - -
352B ASP* 4.7 0.6 - - - +
368B TRP* 3.2 43.1 - - + +
371B THR* 2.8 28.8 + - + +
372B PRO 2.9 18.3 + - - +
373B GLY* 3.5 9.1 - - - +
374B VAL* 3.8 24.0 - - + -
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Residues in contact with LEU 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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113B VAL* 4.2 1.3 - - + -
116B MET* 4.5 14.6 - - + -
140B ILE* 3.5 31.6 - - + -
145B VAL* 4.3 22.4 - - + -
148B PHE* 3.4 56.9 - - + +
149B GLN 4.2 0.9 + - - -
150B GLY* 3.2 21.4 + - - -
316B LYS 3.2 11.6 + - - +
317B ALA* 3.6 6.5 - - - +
318B LEU 3.1 0.6 - - - -
319B ARG* 1.3 76.9 - - - +
321B SER* 1.3 66.8 + - - +
368B TRP* 3.9 20.6 - - + -
371B THR* 5.7 2.2 - - + +
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 4.0 13.2 - - - +
148B PHE* 4.7 3.6 - - - -
149B GLN* 5.4 0.2 - - - +
150B GLY 4.1 3.1 + - - +
274B PHE* 4.1 11.2 + - - -
277B ASN* 3.0 24.1 + - - +
278B THR* 2.9 35.6 + - - +
281B SER* 3.1 16.1 + - - -
282B HIS* 4.8 4.2 - - - -
317B ALA 3.0 17.2 + - - -
318B LEU* 4.0 2.9 - - - -
320B LEU* 1.3 77.6 - - - +
322B GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 322 (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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150B GLY 3.4 16.8 - - - -
151B PRO 4.1 0.2 - - - -
152B PRO* 4.1 1.3 - - - -
277B ASN* 3.3 20.4 + - - -
281B SER* 3.2 16.1 + - - -
291B LEU* 3.8 10.3 - - - +
293B ILE* 4.1 0.7 - - - +
318B LEU* 2.7 22.4 + - - +
320B LEU 3.3 0.8 - - - -
321B SER* 1.3 76.8 - - - +
323B GLY* 1.3 58.8 + - - -
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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