Contacts of the helix formed by residues 293 - 308 (chain C) in PDB entry 5HVO
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 293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ASP 4.5 0.4 + - - -
290C TYR 3.9 6.1 + - - -
291C ILE 3.3 5.5 + - - -
292C LYS* 1.3 77.6 - - - +
294C ILE* 1.3 64.3 + - - +
295C PRO* 3.3 4.5 - - - -
296C GLN* 3.2 23.4 + - - +
297C LYS 3.0 17.3 + - - -
382C SER* 3.3 22.1 - - - -
384C THR* 4.1 7.2 - - - +
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ASP* 4.8 1.6 - - + -
287C ARG 4.4 15.0 - - - +
288C LEU* 3.8 30.7 - - + -
289C ASP 4.5 9.3 + - - +
292C LYS* 4.2 14.4 - - + +
293C GLY* 1.3 73.1 - - - +
295C PRO* 1.3 75.8 - - + +
297C LYS* 3.0 13.0 + - + +
298C LEU* 2.9 34.5 + - + +
319C GLN* 4.2 35.2 - - + +
321C ALA* 5.2 2.5 - - + -
334C LEU* 5.0 1.1 - - + -
338C VAL* 3.9 25.1 - - + -
359C PHE* 6.0 0.2 - - + -
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Residues in contact with PRO 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C ASP 6.1 0.4 - - - +
290C TYR* 5.9 1.8 - - - +
293C GLY* 3.6 4.7 - - - -
294C ILE* 1.3 93.9 - - + +
296C GLN* 1.3 69.0 + - - +
298C LEU* 3.2 2.4 + - + +
299C HIS* 3.0 30.8 + - - -
334C LEU* 4.2 18.2 - - + -
337C VAL* 4.2 22.0 - - + -
338C VAL* 4.3 8.3 - - + -
341C LEU* 3.6 22.9 - - + -
115D ILE* 4.0 20.2 - - + -
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Residues in contact with GLN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLY* 3.2 23.9 - - - +
294C ILE 3.2 0.2 - - - -
295C PRO* 1.3 79.5 - - - +
297C LYS* 1.3 57.8 + - - +
299C HIS* 3.5 2.1 + - - +
300C ALA* 3.0 30.7 + - - +
384C THR* 3.7 11.3 - - - +
426C PRO* 3.3 40.4 - - + +
427C TRP* 3.2 43.5 - - + +
429C THR* 4.8 2.3 - - - +
432C LEU* 3.8 4.0 - - + +
115D ILE* 3.6 34.1 - - + +
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Residues in contact with LYS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER* 3.0 23.1 + - - +
286C ASP* 3.2 20.4 + - - -
292C LYS 4.5 3.8 + - - -
293C GLY 3.0 6.4 + - - +
294C ILE* 3.3 15.3 - - - +
296C GLN* 1.3 77.8 - - - +
298C LEU* 1.3 60.0 + - + +
300C ALA 3.4 0.5 + - - -
301C LEU* 3.0 18.9 + - - +
317C LEU* 3.9 21.1 - - + -
319C GLN* 3.0 29.0 + - - +
380C VAL* 3.8 13.0 + - + -
382C SER* 3.2 32.7 + - - +
432C LEU* 4.0 1.8 - - - -
436C TYR* 2.9 32.4 + - - +
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ILE* 2.9 33.9 + - + +
295C PRO* 3.8 3.1 - - + +
297C LYS* 1.3 78.4 - - + +
299C HIS* 1.3 65.2 + - - +
301C LEU* 3.0 9.1 + - + +
302C GLU 3.0 17.3 + - - -
317C LEU* 3.9 26.7 - - + -
319C GLN* 5.7 2.5 - - + +
338C VAL* 4.3 4.7 - - + +
341C LEU* 4.0 24.2 - - + -
342C VAL* 3.9 27.8 - - + +
345C ILE* 3.3 23.1 - - + +
357C ILE* 4.0 20.9 - - + -
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Residues in contact with HIS 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C PRO* 3.0 21.7 + - + +
296C GLN 3.9 3.6 - - - +
298C LEU* 1.3 76.2 - - - +
300C ALA* 1.3 62.4 + - - +
302C GLU* 3.2 12.3 + - - +
303C VAL* 3.1 26.3 + - - +
341C LEU* 3.5 31.5 - - + +
344C ARG* 3.8 21.3 + - - -
345C ILE* 4.6 0.4 - - - -
429C THR* 3.9 5.4 - - + -
115D ILE* 3.4 31.8 - - + +
116D VAL* 3.3 29.7 - - + +
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C GLN 3.0 16.0 + - - +
297C LYS 3.6 2.7 - - - +
299C HIS* 1.3 73.5 - - - +
301C LEU* 1.3 60.6 + - - +
303C VAL 3.2 0.7 + - - +
304C PHE* 2.8 31.4 + - - +
429C THR* 3.7 19.2 - - + +
432C LEU* 3.3 41.7 - - + -
433C ALA* 3.5 5.1 - - - +
436C TYR* 3.6 7.0 - - + -
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C MET* 5.3 7.9 - - - -
297C LYS 3.0 14.6 + - - +
298C LEU* 3.3 11.2 - - + +
300C ALA* 1.3 77.2 - - - +
302C GLU* 1.3 62.4 + - - +
304C PHE* 3.3 13.8 + - + +
305C LEU* 3.0 36.3 + - + +
315C VAL* 5.4 7.2 - - + -
317C LEU* 4.2 21.8 - - + +
345C ILE* 4.9 2.2 - - + -
356C PRO* 4.1 19.3 - - + +
357C ILE* 3.5 35.0 - - + -
436C TYR* 3.3 22.4 - - + -
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Residues in contact with GLU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU 3.0 11.2 + - - +
299C HIS* 3.5 16.9 - - - +
300C ALA 3.2 0.2 - - - -
301C LEU* 1.3 78.1 - - - +
303C VAL* 1.3 59.1 + - + +
305C LEU 3.4 0.3 + - - -
306C GLN* 3.0 43.0 + - - +
344C ARG* 2.7 38.6 + - - -
345C ILE* 4.2 15.3 - - + +
348C LYS* 2.8 30.1 + - - +
349C PHE* 3.8 22.1 - - + -
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C HIS* 3.1 14.7 + - + +
300C ALA 3.2 6.3 + - - +
302C GLU* 1.3 76.6 - - + +
304C PHE* 1.3 60.4 + - - +
306C GLN* 3.2 15.1 + - - +
307C ASN* 2.8 50.4 + - - +
429C THR* 3.9 16.6 - - + -
430C GLU* 3.6 27.6 - - - +
433C ALA* 3.7 10.3 - - + -
116D VAL* 5.3 7.0 - - + -
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Residues in contact with PHE 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C MET* 6.0 0.7 - - - -
300C ALA 2.8 20.2 + - - +
301C LEU* 3.6 9.2 - - + +
303C VAL* 1.3 72.7 - - - +
305C LEU* 1.3 71.4 + - + +
307C ASN* 3.1 4.6 + - - +
308C HIS* 2.9 47.1 + + - +
311C TRP* 4.0 24.9 - + + -
315C VAL* 3.9 28.3 - - + -
433C ALA* 3.4 28.0 - - + +
436C TYR* 3.8 22.7 - + + -
437C HIS* 3.5 35.7 - + + -
440C VAL* 4.2 9.4 - - + -
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LEU* 3.0 30.5 + - + +
302C GLU* 3.8 4.0 - - - +
304C PHE* 1.3 86.2 - - + +
306C GLN* 1.3 61.1 + - - +
308C HIS 3.4 18.2 - - - +
309C PRO* 3.5 8.3 - - - +
311C TRP* 4.2 1.8 - - + -
312C VAL* 3.8 29.5 - - + +
315C VAL* 3.9 27.4 - - + -
345C ILE* 5.5 0.4 - - + -
349C PHE* 4.0 34.5 - - + -
354C TYR* 4.7 4.3 - - - +
356C PRO* 3.9 28.5 - - + -
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Residues in contact with GLN 306 (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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302C GLU* 3.0 28.1 + - - +
303C VAL* 3.6 15.5 - - - +
305C LEU* 1.3 79.4 - - - +
307C ASN* 1.3 63.7 + - - +
308C HIS 3.4 0.3 + - - -
309C PRO* 3.7 13.3 - - - +
348C LYS* 3.1 36.1 - - - +
349C PHE* 3.9 12.3 - - + -
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Residues in contact with ASN 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C VAL* 2.8 32.7 + - - +
304C PHE* 3.6 1.5 - - - +
306C GLN* 1.3 77.3 - - - +
308C HIS* 1.3 89.6 + - + +
309C PRO* 3.5 6.3 - - - +
310C GLU* 4.3 1.6 - - - +
430C GLU* 3.4 25.2 + - - +
433C ALA* 4.4 7.9 - - - +
434C ARG* 5.7 2.0 - - - +
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Residues in contact with HIS 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C PHE* 2.9 26.9 + + + +
305C LEU* 3.4 7.7 - - - +
307C ASN* 1.3 106.7 + - + +
309C PRO* 1.3 53.3 - - - +
310C GLU* 3.0 31.6 - - - +
311C TRP* 2.8 36.4 + - + +
312C VAL 3.7 2.3 + - - -
433C ALA 5.6 0.4 - - - -
434C ARG* 5.8 2.9 - - - -
437C HIS* 3.7 46.8 + + + -
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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