Contacts of the helix formed by residues 305 - 328 (chain C) in PDB entry 1HYH
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 THR 305 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C THR* 1.3 72.2 - - - +
306C ASP* 1.3 67.1 + - - +
308C GLN* 3.2 8.1 + - + +
309C GLU* 2.9 29.9 + - - +
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Residues in contact with ASP 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C THR* 3.3 6.7 + - - +
305C THR* 1.3 84.7 + - - +
307C GLU* 1.3 57.0 + - + +
309C GLU* 3.2 24.8 + - - +
310C LYS* 2.9 42.3 + - - +
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Residues in contact with GLU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C PHE* 3.4 31.7 - - + -
204C VAL 5.2 0.7 - - - +
205C ALA* 4.1 9.4 - - - -
206C TRP* 3.4 10.0 + - - +
207C SER* 2.6 49.8 + - - -
303C LEU* 3.5 18.5 - - + +
304C THR* 3.1 30.7 + - - +
306C ASP* 1.3 78.1 - - + +
308C GLN* 1.3 62.7 + - - +
310C LYS* 3.2 4.1 + - + -
311C LEU* 3.0 19.5 + - - +
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Residues in contact with GLN 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C MET* 4.7 4.8 - - - +
303C LEU* 4.2 21.3 - - + +
304C THR 2.9 19.3 + - - +
305C THR* 3.5 9.4 - - + +
307C GLU* 1.3 75.8 - - - +
309C GLU* 1.3 61.3 + - - +
311C LEU* 3.3 16.3 + - - +
312C LEU* 3.2 41.4 + - + +
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C THR 2.9 14.0 + - - +
306C ASP* 3.3 30.0 - - - +
308C GLN* 1.3 76.3 - - - +
310C LYS* 1.3 69.4 + - - +
312C LEU* 3.2 8.5 + - - +
313C GLN* 3.1 35.0 + - - +
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Residues in contact with LYS 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C SER* 5.0 2.1 - - - +
203C PHE* 3.8 42.3 - - + +
306C ASP* 2.9 25.4 + - - +
307C GLU* 3.2 8.5 + - + +
309C GLU* 1.3 81.0 - - - +
311C LEU* 1.3 66.5 + - - +
313C GLN* 3.3 19.6 + - - +
314C SER* 3.1 25.5 + - - -
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C LEU* 4.1 14.8 - - + -
196C GLY 4.1 22.4 - - - +
203C PHE* 3.8 8.2 - - + -
280C MET* 4.4 17.0 - - + -
284C LEU* 3.8 18.6 - - + +
286C TYR* 3.8 33.9 - - + -
303C LEU* 4.2 11.7 - - + -
307C GLU 3.0 12.3 + - - +
308C GLN* 3.4 25.1 - - - +
309C GLU 3.2 0.2 - - - -
310C LYS* 1.3 78.1 - - - +
312C LEU* 1.4 61.5 + - - +
314C SER* 3.3 6.2 - - - -
315C ARG* 3.1 21.0 + - - +
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C MET* 3.3 39.0 - - + -
308C GLN* 3.2 25.2 + - + +
309C GLU* 3.8 7.9 - - - +
311C LEU* 1.4 78.4 - - - +
313C GLN* 1.3 64.6 + - - +
315C ARG* 3.2 26.0 + - - +
316C ASP* 3.1 30.9 + - - +
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Residues in contact with GLN 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C SER* 5.4 4.5 - - - -
309C GLU* 3.1 31.0 + - - +
310C LYS* 3.3 21.0 + - - +
312C LEU* 1.3 75.9 - - - +
314C SER* 1.3 57.7 + - - +
316C ASP* 3.3 9.6 + - - +
317C TYR* 3.0 62.1 + - + +
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Residues in contact with SER 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C GLY* 3.6 11.8 - - - -
197C GLU* 3.3 19.6 + - - +
201C SER* 2.7 41.0 + - - -
203C PHE* 4.8 0.9 - - - -
284C LEU* 4.5 2.0 - - - -
310C LYS 3.1 8.9 + - - -
311C LEU 3.3 11.7 - - - -
313C GLN* 1.3 79.1 - - - +
315C ARG* 1.3 56.6 + - - -
317C TYR* 3.2 3.6 + - - +
318C ILE* 3.0 35.0 + - - +
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Residues in contact with ARG 315 (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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279C ASP 4.4 4.6 + - - -
280C MET* 2.6 64.1 + - + +
282C MET* 3.9 16.9 - - + +
284C LEU* 3.8 15.7 - - + +
311C LEU 3.1 9.6 + - - +
312C LEU* 3.5 34.2 - - - +
314C SER* 1.3 80.8 - - - +
316C ASP* 1.3 79.1 + - - +
318C ILE* 3.5 6.5 + - - +
319C GLN* 3.0 31.9 + - - +
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 3.1 19.1 + - - +
313C GLN* 3.6 10.1 - - - +
315C ARG* 1.3 96.3 + - - +
317C TYR* 1.3 72.0 + - + +
319C GLN* 3.2 9.2 + - - +
320C GLN* 3.1 30.6 + - + +
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Residues in contact with TYR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C GLU* 3.7 18.2 - - - +
200C ASN* 4.3 11.2 - - - -
201C SER* 3.5 35.0 - - - -
313C GLN* 3.0 44.2 + - + +
314C SER 3.2 5.1 + - - +
316C ASP* 1.3 78.9 - - + +
318C ILE* 1.3 62.8 + - - +
320C GLN* 3.1 20.4 + - - +
321C ARG* 3.0 27.3 + - + +
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASP* 3.7 29.6 - - + +
147C VAL* 4.2 14.3 - - + +
197C GLU* 3.8 28.9 - - + +
282C MET* 3.2 30.7 - - + -
283C TYR 3.4 22.2 - - - +
284C LEU* 3.9 15.9 - - + -
314C SER 3.0 19.3 + - - +
315C ARG* 3.9 5.4 - - - +
317C TYR* 1.3 73.9 - - - +
319C GLN* 1.3 57.1 + - - +
321C ARG* 3.8 2.0 - - - +
322C PHE* 2.8 32.2 + - - +
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Residues in contact with GLN 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C MET 5.5 0.2 - - - +
281C GLY 4.9 5.2 - - - +
282C MET* 4.0 23.3 + - + +
315C ARG* 3.0 21.2 + - - +
316C ASP* 3.2 13.2 + - - +
318C ILE* 1.3 76.2 - - - +
320C GLN* 1.3 57.6 + - + +
322C PHE* 3.2 14.1 + - - +
323C ASP* 2.9 53.0 + - - +
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Residues in contact with GLN 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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316C ASP* 3.1 21.6 + - + +
317C TYR* 3.5 23.7 - - - +
319C GLN* 1.3 79.0 - - + +
321C ARG* 1.3 67.1 + - + +
323C ASP* 3.3 7.5 + - - +
324C GLU* 3.0 24.5 + - - +
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Residues in contact with ARG 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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144C PRO* 5.8 4.0 - - + -
147C VAL* 3.8 23.6 - - + +
197C GLU* 5.3 5.6 - - - +
317C TYR* 3.0 18.2 + - + +
318C ILE* 4.7 0.9 - - - -
320C GLN* 1.3 78.7 - - + +
322C PHE* 1.3 61.4 + - - +
324C GLU* 3.6 17.4 + - - +
325C ILE* 3.1 24.1 + - - +
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Residues in contact with PHE 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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147C VAL* 4.0 19.5 - - + +
150C ALA* 3.7 24.0 - - + -
151C LEU* 3.6 34.8 - - + -
154C HIS* 4.3 13.0 - - + -
282C MET* 3.7 19.5 - - + -
318C ILE 2.8 20.0 + - - +
319C GLN* 3.5 16.8 - - - +
321C ARG* 1.3 74.6 - - - +
323C ASP* 1.3 66.0 + - - +
325C ILE* 3.2 6.0 + - + +
326C VAL* 2.8 49.1 + - + +
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Residues in contact with ASP 323 (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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319C GLN* 2.9 42.8 + - - +
320C GLN* 3.6 8.8 - - - +
322C PHE* 1.3 79.0 - - - +
324C GLU* 1.3 64.9 + - - +
326C VAL* 3.3 10.4 - - - +
327C ASP* 3.2 32.3 + - - +
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Residues in contact with GLU 324 (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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111C ARG* 2.7 38.5 + - - -
115C LEU* 3.8 16.8 - - + +
320C GLN 3.0 15.5 + - - +
321C ARG* 3.6 17.0 - - - +
323C ASP* 1.3 82.5 - - - +
325C ILE* 1.3 59.7 + - - +
327C ASP* 3.5 16.5 + - - +
328C THR* 3.7 9.7 - - - +
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Residues in contact with ILE 325 (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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115C LEU* 4.1 35.0 - - + +
118C THR* 4.3 18.8 - - + -
119C SER* 4.0 16.1 - - - +
147C VAL* 3.7 21.1 - - + -
148C ILE* 4.6 7.4 - - + -
151C LEU* 4.1 26.2 - - + -
321C ARG 3.1 14.2 + - - +
322C PHE* 3.3 11.0 - - + +
324C GLU* 1.3 71.4 - - - +
326C VAL* 1.3 71.4 + - - +
327C ASP 3.1 1.8 - - - -
328C THR* 2.8 29.3 + - - +
329C LEU 3.9 1.7 + - - -
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 4.2 12.1 - - + -
154C HIS* 3.9 23.3 - - + +
322C PHE* 2.8 37.9 + - + +
323C ASP* 3.3 20.6 - - - +
325C ILE* 1.3 75.3 - - - +
327C ASP* 1.3 69.6 + - - +
328C THR 3.3 0.9 + - - -
329C LEU* 3.3 36.4 + - + +
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LYS* 5.4 0.2 + - - -
323C ASP* 3.2 17.6 + - - +
324C GLU* 3.5 13.5 - - - +
325C ILE 3.1 0.4 - - - -
326C VAL* 1.3 87.0 - - - +
328C THR* 1.3 58.1 + - + +
329C LEU 3.3 4.3 - - - +
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Residues in contact with THR 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 4.2 22.0 - - + -
115C LEU* 3.6 27.0 + - + -
116C LYS* 2.7 47.6 + - - +
119C SER* 2.8 20.8 + - - -
324C GLU 3.7 15.7 - - - +
325C ILE* 2.8 14.0 + - - +
327C ASP* 1.3 79.8 - - + +
329C LEU* 1.3 61.5 + - - +
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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
------------------------------------------------------------
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