Contacts of the helix formed by residues 279 - 299 (chain A) in PDB entry 1R88
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 GLY 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A SER* 4.4 4.0 - - - -
238A ASP* 5.7 2.7 - - - -
241A ALA* 5.7 1.8 - - - -
277A ASP* 3.2 16.4 + - - -
278A ASN* 1.3 76.7 - - - +
280A TRP* 1.3 65.6 + - - -
281A GLY 3.2 2.2 - - - -
282A SER* 3.1 13.3 + - - -
283A TRP* 3.1 35.1 + - - -
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Residues in contact with TRP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.4 22.0 - - - -
67A ALA* 4.5 7.7 - - + +
69A ASN* 5.5 1.6 + - - -
76A ASN* 3.5 22.2 - - + +
77A TRP* 3.5 66.2 - + - -
80A ALA* 3.8 26.1 - - + +
81A GLY* 3.8 17.7 - - - -
144A ALA* 4.9 1.1 - - + -
237A SER* 5.0 2.4 + - - -
238A ASP* 5.8 6.7 + - + -
241A ALA* 5.3 5.9 - - + +
277A ASP* 4.4 0.4 + - - -
279A GLY* 1.3 71.0 - - - -
281A GLY* 1.3 64.1 + - - +
282A SER 3.1 0.2 - - - -
283A TRP* 3.5 35.1 - + + -
284A ALA* 3.1 27.9 + - - +
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER* 5.6 0.6 + - - -
277A ASP* 4.7 7.6 + - - -
279A GLY 3.2 1.8 + - - -
280A TRP* 1.3 77.1 - - - +
282A SER* 1.3 57.2 + - - +
285A PRO* 3.2 19.4 - - - +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TRP* 3.4 21.2 - - - -
276A GLY* 3.9 6.8 - - - -
277A ASP* 3.1 44.2 + - - +
279A GLY 3.1 2.8 + - - -
281A GLY* 1.3 77.0 - - - +
283A TRP* 1.3 63.0 + - - +
284A ALA 3.4 2.7 - - - -
285A PRO* 3.3 7.1 - - - +
286A GLN* 3.1 25.1 + - - +
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Residues in contact with TRP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA* 3.9 23.6 - - + -
77A TRP* 3.8 6.6 - - + -
144A ALA* 3.5 26.9 - - + -
145A ALA* 4.5 1.3 - - + -
168A MET* 3.5 38.7 - - + +
169A SER* 3.1 25.9 + - - -
229A TRP* 3.7 13.3 - + - -
241A ALA* 4.2 8.7 - - + -
242A MET* 3.7 22.2 - - - -
278A ASN 3.5 9.4 - - - -
279A GLY* 3.1 43.1 + - - +
280A TRP* 3.3 40.1 + + + -
282A SER* 1.3 73.0 - - - +
284A ALA* 1.3 64.9 + - - +
286A GLN* 3.3 0.7 + - - -
287A LEU 3.1 18.4 + - - -
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 4.6 1.3 - - - -
80A ALA 3.8 15.9 - - - +
81A GLY* 3.7 27.2 - - - +
82A ASN* 4.8 5.8 - - + -
86A THR* 4.7 5.5 + - - +
280A TRP* 3.1 15.0 + - - +
283A TRP* 1.3 77.3 - - - +
285A PRO* 1.3 70.6 - - + +
287A LEU* 3.2 18.5 + - - +
288A GLY 3.6 3.3 + - - -
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Residues in contact with PRO 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLY* 3.2 26.9 - - - +
282A SER* 3.3 13.2 - - - +
284A ALA* 1.3 95.7 - - + +
286A GLN* 1.3 53.9 + - - -
288A GLY* 3.2 5.5 + - - +
289A ALA* 3.1 23.8 + - - +
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Residues in contact with GLN 286 (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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168A MET* 3.8 19.7 - - + -
227A TRP* 3.1 38.6 - - - +
229A TRP* 3.3 47.4 + - + -
271A ASP* 4.7 5.9 + - - +
282A SER 3.1 21.3 + - - +
283A TRP* 3.6 5.6 - - - +
284A ALA 3.2 0.4 - - - -
285A PRO* 1.3 72.3 - - - +
287A LEU* 1.3 65.1 + - - +
289A ALA* 3.2 13.0 + - - +
290A MET* 3.1 24.0 + - + +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.0 20.9 - - + -
77A TRP* 3.8 22.4 - - + -
81A GLY 4.3 2.9 - - - +
83A ALA* 3.8 31.9 - - + -
86A THR* 4.0 9.9 - - + -
87A LEU* 4.0 22.4 - - + -
142A VAL* 4.4 15.0 - - + -
168A MET* 3.6 5.7 - - + +
283A TRP 3.1 11.8 + - - +
284A ALA 3.2 10.5 + - - +
286A GLN* 1.3 75.9 - - - +
288A GLY* 1.3 61.7 + - - +
290A MET* 3.4 5.0 + - + +
291A SER* 3.1 23.9 + - - -
294A ILE* 4.5 13.7 - - + -
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.5 22.5 - - - +
284A ALA 3.6 2.8 + - - -
285A PRO* 3.2 9.3 + - - -
287A LEU* 1.3 79.8 - - - +
289A ALA* 1.3 59.1 + - - +
291A SER* 3.0 21.4 + - - -
292A GLY 4.7 0.3 + - - -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TRP* 3.8 12.5 - - + -
285A PRO 3.1 12.1 + - - +
286A GLN* 3.2 26.4 + - - +
288A GLY* 1.3 77.9 - - - +
290A MET* 1.3 57.8 + - - +
291A SER 3.7 0.2 + - - -
292A GLY* 4.6 3.5 + - - -
293A ASP 5.2 1.0 + - - -
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Residues in contact with MET 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 3.9 24.5 - - + -
164A PHE* 4.3 6.5 - - - -
166A GLY* 4.6 5.8 - - - -
168A MET* 3.6 31.9 - - + -
227A TRP* 3.1 74.0 - - + +
286A GLN* 3.1 14.1 + - + +
287A LEU* 3.7 7.4 - - - +
289A ALA* 1.3 74.8 - - - +
291A SER* 1.3 65.8 + - - +
292A GLY 3.3 2.5 - - - -
293A ASP* 3.0 6.0 + - - +
294A ILE* 3.0 41.9 + - + +
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 4.9 1.1 - - - -
87A LEU* 3.9 20.1 - - - +
90A LYS* 3.9 25.6 + - - -
287A LEU 3.1 17.2 + - - -
288A GLY* 3.0 18.1 + - - -
289A ALA 3.4 1.0 - - - -
290A MET* 1.3 75.6 - - - +
292A GLY* 1.3 65.5 + - - +
294A ILE* 3.2 12.0 + - - +
295A VAL* 3.1 29.2 + - - +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 6.2 0.9 - - - -
288A GLY 4.7 0.2 + - - -
289A ALA 4.6 3.2 + - - -
290A MET 3.3 0.4 - - - -
291A SER* 1.3 82.0 + - - +
293A ASP* 1.3 57.4 + - - +
295A VAL* 3.6 6.2 + - - +
296A GLY* 3.0 23.7 + - - -
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Residues in contact with ASP 293 (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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164A PHE* 3.4 18.0 - - + -
225A ARG* 2.9 40.9 + - - +
227A TRP* 3.5 33.7 - - + +
289A ALA 5.2 1.2 + - - +
290A MET 3.0 11.2 + - - +
292A GLY* 1.3 75.4 - - - +
294A ILE* 1.3 64.2 + - - +
296A GLY* 3.5 1.6 + - - -
297A ALA* 3.2 23.6 + - - +
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Residues in contact with ILE 294 (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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62A VAL* 4.2 9.6 - - + -
87A LEU* 4.9 5.6 - - + -
92A ILE* 3.7 24.2 - - + -
140A ALA* 4.0 21.8 - - + -
142A VAL* 4.1 11.7 - - + -
164A PHE* 3.7 27.8 - - + -
287A LEU* 4.5 11.2 - - + -
290A MET* 3.0 40.7 + - + +
291A SER* 3.6 12.6 - - - +
293A ASP* 1.3 76.0 - - - +
295A VAL* 1.3 62.4 + - - +
297A ALA* 3.1 4.3 + - - +
298A ILE* 3.1 26.8 + - + +
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Residues in contact with VAL 295 (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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87A LEU* 6.3 0.2 - - + -
90A LYS* 3.7 34.5 - - + +
92A ILE* 4.0 24.2 - - + -
291A SER 3.1 17.9 + - - +
292A GLY* 3.9 6.7 - - - +
294A ILE* 1.3 77.0 - - - +
296A GLY* 1.3 58.1 + - - +
299A ARG* 3.0 69.1 + - + +
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Residues in contact with GLY 296 (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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292A GLY 3.0 17.4 + - - -
293A ASP* 4.0 2.7 - - - -
294A ILE 3.3 0.4 - - - -
295A VAL* 1.3 77.7 - - - +
297A ALA* 1.3 60.8 + - - +
299A ARG 4.9 4.7 + - - -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLY 5.2 1.8 - - - +
164A PHE* 3.7 23.8 - - + -
225A ARG* 4.3 14.8 - - + -
293A ASP 3.2 16.7 + - - +
294A ILE 3.1 5.9 + - - +
296A GLY* 1.3 79.6 - - - +
298A ILE* 1.3 63.3 + - + +
299A ARG 5.3 0.4 - - - -
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 3.0 32.5 + - + -
61A ALA 3.5 37.5 - - - +
92A ILE* 3.8 26.5 - - + -
138A GLY 3.3 22.8 - - - +
139A HIS 3.9 14.6 - - - +
140A ALA* 4.0 9.4 - - + +
163A GLY* 5.3 2.0 - - - -
164A PHE* 4.1 4.9 - - + +
294A ILE* 3.1 31.6 + - + +
297A ALA* 1.3 85.7 - - + +
299A ARG* 1.3 64.7 + - - +
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Residues in contact with ARG 299 (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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60A HIS* 4.9 5.0 - - - -
90A LYS* 3.2 26.7 + - - +
91A GLY* 3.5 25.9 - - - +
92A ILE* 3.9 14.8 - - + -
295A VAL* 3.0 35.2 + - + +
296A GLY 5.0 4.9 - - - -
297A ALA 5.3 0.4 - - - -
298A ILE* 1.3 82.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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