Contacts of the helix formed by residues 305 - 313 (chain A) in PDB entry 1RQG
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 ILE 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A MET* 3.9 9.0 - - + -
199A LEU* 3.8 15.7 - - + +
216A VAL* 3.9 21.8 - - + +
219A TRP* 4.3 23.1 - - + -
220A ILE* 3.8 27.8 - - + -
224A LEU* 4.7 10.5 - - + -
301A PRO* 2.8 21.3 + - + +
303A HIS 3.5 1.4 - - - -
304A ALA* 1.3 86.3 - - - +
306A PHE* 1.3 89.9 + - + +
308A PRO* 3.1 14.7 - - - +
309A ALA* 3.2 16.6 + - - +
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Residues in contact with PHE 306 (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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192A MET* 3.3 34.5 - - + -
219A TRP* 5.1 13.7 - + - -
224A LEU* 5.3 7.6 - - + -
227A ARG* 4.1 26.5 - - + -
254A TRP* 3.7 23.6 - + + -
301A PRO* 4.1 15.3 - - + -
302A PHE* 3.3 27.5 + + + +
305A ILE* 1.3 90.7 - - + +
307A TRP* 1.3 60.8 + - - +
309A ALA* 3.1 2.3 + - - +
310A PHE* 2.8 53.4 + - + -
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Residues in contact with TRP 307 (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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107A PHE* 4.8 2.7 - + - -
258A PRO* 3.1 50.9 - - + -
259A ILE* 3.9 13.0 - - + -
261A TYR* 4.1 8.3 - + + -
262A ILE* 4.2 13.7 - - + -
282A TRP* 4.5 15.7 - + - -
293A HIS* 3.0 26.9 + - - -
302A PHE* 2.8 33.8 + - + +
303A HIS* 3.9 21.3 - - - +
306A PHE* 1.3 73.2 - - - +
308A PRO* 1.3 61.4 - - + +
310A PHE* 3.3 15.5 + + + +
311A LEU* 3.2 54.7 + - + +
329A PRO* 3.9 19.6 - - + +
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Residues in contact with PRO 308 (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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199A LEU* 4.0 14.1 - - + -
202A TRP* 3.9 19.7 - - + -
303A HIS 3.3 22.0 - - - +
304A ALA 3.7 11.9 - - - -
305A ILE 3.1 17.9 - - - +
307A TRP* 1.3 95.5 - - + +
309A ALA* 1.3 55.6 + - - +
311A LEU* 3.0 17.9 + - + +
312A MET* 2.9 30.5 + - - +
328A LEU* 4.5 11.5 - - + +
329A PRO* 4.2 6.7 - - + -
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Residues in contact with ALA 309 (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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190A ILE* 5.0 1.3 - - + -
192A MET* 3.7 25.4 - - + -
195A PHE* 4.0 24.9 - - + -
199A LEU* 4.3 2.8 - - + +
305A ILE 3.2 11.2 + - - +
306A PHE 3.1 8.2 + - - +
308A PRO* 1.3 74.1 - - - +
310A PHE* 1.3 58.8 + - + +
311A LEU 3.0 1.1 - - - -
312A MET* 2.9 14.2 + - - +
313A ALA* 2.7 36.5 + - - +
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Residues in contact with PHE 310 (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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107A PHE* 3.5 21.2 - - + +
190A ILE* 4.0 19.7 - - + -
192A MET* 4.7 3.1 - - - -
254A TRP* 3.5 49.8 - + - -
255A PHE* 3.7 55.8 - + + +
258A PRO* 4.6 0.7 - - + -
259A ILE* 5.8 0.4 - - + -
302A PHE* 4.0 12.3 - + - -
306A PHE* 2.8 39.9 + - + -
307A TRP* 3.4 24.7 - + + +
309A ALA* 1.3 72.6 - - + +
311A LEU* 1.3 63.1 + - - +
313A ALA* 3.5 14.5 + - - +
314A TYR 3.6 5.2 + - - -
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Residues in contact with LEU 311 (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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107A PHE* 3.6 20.2 - - + -
262A ILE* 4.3 4.5 - - + -
282A TRP* 6.0 2.5 - - + -
307A TRP* 3.2 61.7 + - + +
308A PRO* 3.0 13.8 + - + +
309A ALA 3.0 0.6 - - - -
310A PHE* 1.3 77.7 - - - +
312A MET* 1.3 62.1 + - - +
314A TYR* 3.2 18.5 + - - +
315A GLY* 4.1 0.7 + - - -
326A TRP* 3.8 28.0 - - + +
327A ASN 3.5 22.0 - - - +
328A LEU* 4.0 19.5 - - + -
329A PRO* 4.7 1.6 - - + -
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Residues in contact with MET 312 (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 HIS* 5.2 1.4 + - - -
195A PHE* 3.6 26.0 - - + -
198A ARG* 3.7 64.6 - - + +
199A LEU* 3.9 30.3 - - + -
202A TRP* 4.8 4.3 - - + -
308A PRO 2.9 15.0 + - - +
309A ALA* 2.9 7.4 + - - +
311A LEU* 1.3 71.4 - - - +
313A ALA* 1.3 52.9 + - - +
314A TYR 2.9 4.9 - - - -
315A GLY* 2.6 32.0 + - - +
328A LEU* 3.8 30.3 - - + -
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Residues in contact with ALA 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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107A PHE 5.7 0.7 - - - +
110A LYS 3.5 12.3 - - - +
111A ALA* 4.4 17.3 - - + -
114A ASN* 3.4 16.8 - - - +
116A HIS* 3.9 16.7 - - + -
190A ILE* 4.5 7.6 - - + -
195A PHE* 3.6 24.4 - - + -
255A PHE* 6.4 1.1 - - + -
309A ALA 2.7 19.0 + - - +
310A PHE* 3.7 10.5 - - - +
312A MET* 1.3 71.8 - - - +
314A TYR* 1.3 55.7 + - - +
315A GLY 3.1 1.6 - - - -
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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
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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