Contacts of the helix formed by residues 310 - 322 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ARG* 3.5 22.1 - - - +
135C LEU 3.0 10.6 + - - +
136C GLU* 3.7 17.0 - - - +
302C ASP* 4.2 0.4 - - - -
309C MET* 1.3 75.6 - - - +
311C PHE* 1.3 82.1 + - + +
312C ARG* 3.0 62.7 + - - +
313C VAL* 3.1 18.0 + - - +
314C LEU* 3.7 4.7 + - - +
341C ILE* 3.5 21.9 - - + +
345C PHE* 4.1 10.3 - + - -
473C ASP* 3.1 36.8 + - - -
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Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C TYR* 4.1 17.0 - - - -
295C ARG* 3.6 34.5 - - + +
298C HIS* 4.2 3.6 - - + -
302C ASP* 3.4 30.7 - - - +
310C HIS* 1.3 85.7 + - + +
312C ARG* 1.3 57.6 + - - +
314C LEU* 3.0 14.8 + - + -
315C ALA* 2.8 39.3 + - + -
326C ILE* 3.9 16.6 - - + -
327C HIS 3.5 22.2 - - - -
328C SER* 4.6 0.9 - - - -
345C PHE* 3.7 39.3 - + + -
349C LEU* 5.1 3.1 - - + -
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Residues in contact with ARG 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLU* 2.8 68.6 + - - +
137C ASP* 3.9 19.5 - - - +
310C HIS* 3.0 41.9 + - - +
311C PHE* 1.3 76.4 - - - +
313C VAL* 1.3 57.2 + - - +
315C ALA* 3.6 3.5 - - - +
316C LYS* 3.1 33.6 + - - +
341C ILE* 4.2 10.9 + - - +
344C GLY 6.3 0.4 - - - -
345C PHE* 3.8 30.3 - - + +
348C LEU* 4.2 13.7 - - + +
360C ARG 4.0 6.7 + - - -
361C GLY* 3.0 42.8 + - - -
362C ILE* 4.9 2.1 - - - +
363C TYR* 4.4 0.8 - - - -
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C MET* 6.0 0.3 - - - +
117C PHE* 3.8 14.5 - - + -
135C LEU* 4.0 15.9 - - + +
136C GLU 3.5 29.8 - - - +
137C ASP* 3.8 15.3 - - - +
138C LEU* 4.0 17.4 - - + +
309C MET* 3.7 26.5 - - + -
310C HIS 3.1 11.0 + - - +
311C PHE 3.0 0.8 - - - -
312C ARG* 1.3 76.9 - - - +
314C LEU* 1.3 60.3 + - - +
316C LYS* 3.3 9.1 + - - +
317C ALA* 3.0 27.0 + - - +
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PHE* 4.5 11.4 - - + -
269C TYR* 3.0 27.1 + - - +
270C LEU* 4.4 22.9 - - + -
274C PHE* 4.9 2.2 - - + -
298C HIS* 4.2 21.5 - - + +
301C ILE* 4.6 17.9 - - + -
302C ASP* 4.1 20.2 - - + +
309C MET* 4.1 28.3 - - + +
310C HIS 4.2 6.7 - - - +
311C PHE* 3.0 14.6 + - + +
313C VAL* 1.3 77.6 - - - +
315C ALA* 1.3 61.4 + - - +
317C ALA* 3.5 6.5 + - - +
318C LEU* 3.2 15.6 + - - +
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C PHE* 2.8 33.5 + - + +
312C ARG* 3.6 9.9 - - - +
314C LEU* 1.3 76.7 - - - +
316C LYS* 1.3 66.0 + - + +
318C LEU* 3.2 4.9 + - - +
319C ARG* 3.1 17.5 + - - +
326C ILE* 4.4 8.5 - - - -
345C PHE* 4.8 5.2 - - + +
348C LEU* 6.1 1.6 - - + -
349C LEU* 3.7 34.4 - - + +
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Residues in contact with LYS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASP* 3.1 21.8 + - - +
138C LEU* 2.6 35.1 + - + +
139C ARG* 4.6 1.0 - - - +
140C ILE* 4.3 15.7 - - + -
312C ARG 3.1 20.0 + - - +
313C VAL* 3.3 6.3 + - + +
315C ALA* 1.3 76.4 - - - +
317C ALA* 1.3 61.9 + - - +
319C ARG* 3.3 4.9 + - - +
320C LEU* 3.2 27.4 + - - +
348C LEU* 4.0 35.5 - - + +
349C LEU* 5.6 0.2 - - - -
362C ILE* 6.1 0.2 - - - +
364C PHE* 5.1 3.2 + - - +
366C GLN* 3.0 30.4 + - - +
368C TRP* 4.1 23.9 - - + -
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Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 3.6 18.6 - - + +
116C MET* 4.9 5.1 - - + +
117C PHE* 3.6 30.5 - - + -
140C ILE* 5.4 0.2 - - - +
274C PHE* 3.9 8.3 - - + -
313C VAL 3.0 17.0 + - - +
314C LEU 3.6 6.5 - - - +
316C LYS* 1.3 78.4 - - - +
318C LEU* 1.3 56.7 + - - +
320C LEU* 3.3 7.9 + - - +
321C SER* 3.0 29.1 + - - -
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C TYR* 3.7 34.5 - - + -
277C ASN* 3.8 11.4 - - - +
293C ILE* 3.8 16.8 - - + -
314C LEU 3.2 6.7 + - - +
315C ALA 3.2 7.4 + - - +
317C ALA* 1.3 77.1 - - - +
319C ARG* 1.3 61.3 + - - +
321C SER* 4.5 2.5 - - - +
322C GLY* 2.7 46.1 + - - +
323C GLY* 4.0 23.3 - - - +
325C HIS 4.6 0.2 - - - +
326C ILE* 3.7 34.5 - - + -
349C LEU* 5.5 0.4 - - + -
374C VAL* 4.6 6.1 - - + -
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Residues in contact with ARG 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C GLY* 3.3 19.8 - - - -
151C PRO* 3.3 5.2 - - + +
315C ALA 3.1 12.4 + - - +
316C LYS* 3.3 8.9 + - - +
318C LEU* 1.3 78.6 - - - +
320C LEU* 1.3 59.3 + - - +
348C LEU 2.8 25.0 + - - -
349C LEU* 3.3 25.3 + - + +
350C ARG 4.1 0.8 + - - -
351C ASP 2.8 32.1 + - - -
352C ASP* 4.7 0.8 - - - +
368C TRP* 3.2 41.3 - - + +
371C THR* 2.8 31.5 + - + +
372C PRO 3.0 18.1 + - - +
373C GLY* 3.6 8.5 - - - +
374C VAL* 3.9 22.0 - - + -
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 4.0 8.1 - - + -
116C MET* 4.7 9.0 - - + -
140C ILE* 3.5 33.2 - - + -
145C VAL* 4.3 23.6 - - + -
148C PHE* 3.5 55.8 - - + +
149C GLN 4.3 0.5 + - - -
150C GLY* 3.3 21.2 + - - -
316C LYS 3.2 11.5 + - - +
317C ALA* 3.6 6.5 - - - +
318C LEU 3.1 0.4 - - - -
319C ARG* 1.3 76.1 - - - +
321C SER* 1.3 66.3 + - - +
368C TRP* 3.9 20.4 - - + -
371C THR* 5.7 2.2 - - + +
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Residues in contact with SER 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 4.0 12.7 - - - +
148C PHE* 4.8 4.0 - - - -
149C GLN* 5.4 0.2 - - - +
150C GLY 4.1 2.9 + - - +
274C PHE* 4.0 14.0 + - - -
277C ASN* 3.1 22.6 + - - +
278C THR* 2.9 37.1 + - - +
281C SER* 3.1 17.2 + - - -
282C HIS* 4.8 3.5 + - - -
317C ALA 3.0 16.6 + - - -
318C LEU* 4.1 3.1 - - - -
320C LEU* 1.3 77.4 - - - +
322C GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLY 3.4 18.6 - - - -
151C PRO 4.0 0.7 - - - -
152C PRO* 4.0 1.3 - - - -
277C ASN* 3.3 20.8 + - - -
281C SER* 3.3 14.5 + - - -
291C LEU* 3.7 9.8 - - - +
293C ILE* 4.2 0.5 - - - +
318C LEU* 2.7 21.8 + - - +
320C LEU 3.2 1.0 - - - -
321C SER* 1.3 76.3 - - - +
323C GLY* 1.3 57.5 + - - -
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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