Contacts of the helix formed by residues 310 - 322 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D ARG* 3.6 21.7 - - - +
135D LEU 3.0 12.4 + - - +
136D GLU* 3.8 14.4 - - - +
302D ASP* 4.2 0.4 - - - -
309D MET* 1.3 75.2 - - - +
311D PHE* 1.3 82.5 + - + +
312D ARG* 3.0 60.5 + - - +
313D VAL* 3.0 18.4 + - - +
314D LEU* 3.6 4.7 + - - +
341D ILE* 3.5 21.9 - - + +
345D PHE* 4.2 11.2 - + - -
473D ASP* 3.0 37.0 + - - -
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Residues in contact with PHE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D TYR* 4.3 15.9 - - - -
295D ARG* 3.5 39.5 - - + +
298D HIS* 4.2 3.4 - - + -
302D ASP* 3.4 32.2 - - - +
310D HIS* 1.3 85.1 + - + +
312D ARG* 1.3 57.9 + - - +
314D LEU* 3.0 13.4 + - + -
315D ALA* 2.8 39.3 + - + -
326D ILE* 4.0 16.2 - - + -
327D HIS 3.4 23.1 - - - -
328D SER* 4.5 1.1 - - - -
345D PHE* 3.8 36.8 - + + -
349D LEU* 5.2 2.7 - - + -
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Residues in contact with ARG 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLU* 2.7 67.9 + - - +
137D ASP* 3.9 19.1 - - - +
310D HIS* 3.0 41.5 + - + +
311D PHE* 1.3 77.3 - - - +
313D VAL* 1.3 58.4 + - + +
315D ALA* 3.5 2.9 + - - +
316D LYS* 3.1 32.4 + - - +
341D ILE* 4.2 15.2 + - - +
345D PHE* 3.9 30.2 - - + +
348D LEU* 4.3 14.7 - - + +
360D ARG 4.2 2.6 + - - -
361D GLY* 3.0 43.1 + - - -
362D ILE* 4.9 2.1 - - - +
363D TYR* 4.1 1.0 - - - -
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Residues in contact with VAL 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D MET* 5.9 0.2 - - - +
117D PHE* 3.7 27.1 - - + -
135D LEU* 3.9 17.7 - - + +
136D GLU 3.6 25.4 - - - +
137D ASP* 3.8 18.6 - - - +
138D LEU* 3.9 17.7 - - + +
309D MET* 3.7 13.9 - - + -
310D HIS 3.0 10.0 + - - +
312D ARG* 1.3 76.9 - - - +
314D LEU* 1.3 65.2 + - - +
316D LYS* 3.4 8.7 + - + +
317D ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D PHE* 4.7 10.1 - - + -
269D TYR* 3.0 25.7 + - - +
270D LEU* 4.4 23.6 - - + -
274D PHE* 4.8 2.7 - - + -
298D HIS* 4.3 17.5 - - + +
301D ILE* 4.6 18.2 - - + -
302D ASP* 4.0 22.9 - - + +
309D MET* 4.0 27.8 - - + +
310D HIS 3.6 6.9 + - - +
311D PHE* 3.0 18.5 + - + +
313D VAL* 1.3 78.0 - - - +
315D ALA* 1.3 61.8 + - - +
317D ALA* 3.5 5.8 + - - +
318D LEU* 3.1 15.8 + - - +
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D PHE* 2.8 34.0 + - + +
312D ARG* 3.7 8.5 - - - +
314D LEU* 1.3 75.5 - - - +
316D LYS* 1.3 64.6 + - + +
318D LEU* 3.1 4.5 + - - +
319D ARG* 3.1 18.2 + - - +
326D ILE* 4.4 9.6 - - + -
345D PHE* 4.8 5.8 - - + +
348D LEU* 6.2 1.8 - - + -
349D LEU* 3.8 33.7 - - + +
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASP* 3.0 23.0 + - - +
138D LEU* 2.6 34.2 + - + +
139D ARG* 4.6 0.8 - - - +
140D ILE* 4.1 18.6 - - + -
312D ARG 3.1 21.1 + - - +
313D VAL* 3.8 7.0 - - + +
315D ALA* 1.3 75.0 - - - +
317D ALA* 1.3 63.1 + - - +
319D ARG* 3.2 5.5 + - - +
320D LEU* 3.2 27.8 + - - +
348D LEU* 3.9 36.6 - - + +
349D LEU* 5.5 0.4 - - - -
364D PHE* 5.1 3.2 + - - +
366D GLN* 3.1 29.8 + - - +
368D TRP* 4.0 20.6 - - + -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 3.6 12.4 - - + +
116D MET* 4.8 4.0 - - + +
117D PHE* 3.5 30.7 - - + -
140D ILE* 5.4 0.2 - - - +
274D PHE* 3.9 13.2 - - + -
313D VAL 3.0 17.7 + - - +
314D LEU 3.5 7.0 - - - +
315D ALA 3.2 0.2 - - - -
316D LYS* 1.3 78.4 - - - +
318D LEU* 1.3 57.1 + - - +
320D LEU* 3.3 8.4 + - - +
321D SER* 2.9 29.5 + - - -
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D TYR* 3.6 30.0 - - + -
277D ASN* 3.9 9.2 - - - +
293D ILE* 3.8 17.9 - - + -
314D LEU 3.1 14.3 + - - +
315D ALA 3.1 8.5 + - - +
317D ALA* 1.3 75.0 - - - +
319D ARG* 1.3 60.8 + - - +
321D SER* 4.4 2.2 - - - +
322D GLY* 2.7 46.7 + - - +
323D GLY* 4.0 22.7 - - - +
325D HIS 4.5 0.2 - - - +
326D ILE* 3.6 36.6 - - + -
349D LEU* 5.6 0.7 - - + -
374D VAL* 4.5 5.8 - - + -
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Residues in contact with ARG 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLY* 3.3 19.4 - - - -
151D PRO* 3.3 6.3 - - + +
315D ALA 3.1 11.8 + - - +
316D LYS* 3.2 9.1 + - - +
318D LEU* 1.3 77.0 - - - +
320D LEU* 1.3 60.1 + - - +
348D LEU 2.9 23.5 + - - -
349D LEU* 3.3 27.1 + - + +
350D ARG 3.9 2.2 + - - -
351D ASP 2.8 31.3 + - - -
352D ASP* 4.6 0.8 - - - +
368D TRP* 3.3 43.0 - - + +
371D THR* 2.8 30.5 + - + +
372D PRO 3.0 20.5 + - - +
373D GLY* 3.7 5.1 - - - +
374D VAL* 3.8 23.1 - - + -
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 4.1 6.7 - - + -
116D MET* 4.7 10.3 - - + -
140D ILE* 3.6 32.5 - - + -
145D VAL* 4.3 23.1 - - + -
148D PHE* 3.6 56.3 - - + +
149D GLN 4.3 0.5 + - - -
150D GLY* 3.3 21.0 + - - -
316D LYS 3.2 10.9 + - - +
317D ALA* 3.6 5.8 - - - +
318D LEU 3.1 0.6 - - - -
319D ARG* 1.3 75.3 - - - +
321D SER* 1.3 68.0 + - - +
368D TRP* 3.9 21.8 - - + -
371D THR* 5.6 2.5 - - + -
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Residues in contact with SER 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 4.0 13.9 - - - +
148D PHE* 4.8 3.4 - - - -
149D GLN* 5.4 0.5 - - - +
150D GLY 4.2 2.3 + - - +
274D PHE* 4.1 11.7 + - - -
277D ASN* 2.9 25.3 + - - +
278D THR* 2.9 36.3 + - - +
281D SER* 3.1 17.2 + - - -
282D HIS* 5.1 2.8 + - - -
317D ALA 2.9 16.5 + - - -
318D LEU* 4.0 3.4 - - - -
320D LEU* 1.3 77.5 - - - +
322D GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLY 3.5 17.5 - - - -
151D PRO 4.1 0.4 - - - -
152D PRO* 4.0 1.3 - - - -
277D ASN* 3.3 20.4 + - - -
281D SER* 3.3 15.3 + - - -
291D LEU* 3.7 10.8 - - - +
293D ILE* 4.2 0.5 - - - +
318D LEU* 2.7 22.0 + - - +
320D LEU 3.2 1.2 - - - -
321D SER* 1.3 75.4 - - - +
323D GLY* 1.3 58.0 + - - -
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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