Contacts of the helix formed by residues 304 - 323 (chain C) in PDB entry 7CAL
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 SER 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C VAL* 3.2 18.9 + - - -
301C HIS* 4.2 8.5 + - - -
302C TRP 3.5 2.5 + - - -
303C THR* 1.3 77.6 - - - +
305C ARG* 1.3 68.2 + - - +
306C THR 3.5 0.2 - - - -
307C ARG* 3.9 18.6 - - - +
308C THR* 3.3 30.5 + - - +
346C LEU* 4.3 3.6 - - - +
311D ASP* 5.0 5.2 + - - -
314D ARG* 4.4 11.3 + - - -
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Residues in contact with ARG 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C TRP 4.7 4.8 + - - +
303C THR* 3.4 1.0 - - - +
304C SER* 1.3 84.5 - - - +
306C THR* 1.3 65.3 + - - +
308C THR* 3.9 2.4 + - - -
309C PHE* 3.4 22.2 + - - +
341C PHE* 3.5 37.6 + - + -
345C GLY* 4.0 26.5 - - - -
346C LEU* 4.0 22.8 - - + +
314D ARG* 4.8 21.3 - - - +
318D GLU* 3.9 29.9 + - - -
322D ARG* 5.1 2.6 - - - +
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Residues in contact with THR 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 4.3 29.7 + - + +
187B LYS* 4.1 27.0 - - + +
193B TYR* 4.4 13.6 - - + -
303C THR* 4.3 9.5 + - - +
304C SER 3.5 0.4 - - - -
305C ARG* 1.3 79.0 + - - +
307C ARG* 1.3 59.3 + - - +
309C PHE* 4.0 10.4 - - + +
310C ARG* 3.3 24.8 + - - +
341C PHE* 4.6 6.2 - - + -
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 4.3 15.9 + - + +
297B ASN* 2.9 36.3 + - - +
298B LEU* 6.2 0.2 - - - -
300B VAL* 5.0 13.5 - - - +
301B HIS* 3.6 47.9 + - + +
300C VAL* 4.3 16.4 + - - +
303C THR 3.3 18.2 + - - +
304C SER* 3.9 25.9 + - - +
305C ARG 3.3 0.6 - - - -
306C THR* 1.3 76.9 - - - +
308C THR* 1.3 72.5 + - - +
309C PHE 3.2 1.3 - - - -
310C ARG* 3.3 2.6 + - - -
311C ASP* 3.1 25.4 + - - +
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Residues in contact with THR 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C SER* 3.3 17.7 + - - +
307C ARG* 1.3 91.0 - - - +
309C PHE* 1.3 65.0 + - - +
311C ASP* 3.7 13.4 - - - +
312C SER* 3.4 20.3 + - - -
346C LEU* 3.3 34.0 - - + +
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Residues in contact with PHE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 4.0 24.2 - - + -
189B ILE* 4.2 11.9 - - + -
305C ARG 3.4 17.0 + - - +
306C THR* 4.0 9.6 - - + +
307C ARG 3.2 0.2 - - - -
308C THR* 1.3 82.5 + - - +
310C ARG* 1.3 80.9 + - + +
311C ASP 3.2 0.4 - - - -
312C SER* 3.2 7.4 + - - -
313C VAL* 3.2 47.8 + - + +
337C ILE* 4.0 15.7 - - + -
338C CYS* 4.2 11.9 - - - -
341C PHE* 3.8 53.2 - + + -
346C LEU* 4.5 3.8 - - + +
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Residues in contact with ARG 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 4.2 1.4 + - - -
186B GLU* 2.4 41.4 + - - +
187B LYS 4.1 0.6 - - - -
188B ASP 3.1 21.6 + - - +
189B ILE* 4.1 16.3 + - - +
191B PHE 2.4 28.5 + - - -
192B ASN* 4.1 7.5 + - - +
193B TYR* 4.1 30.7 - - + +
301B HIS* 4.6 8.5 + - + -
306C THR 3.3 17.8 + - - +
307C ARG 3.3 6.9 + - - +
309C PHE* 1.3 96.9 - - + +
311C ASP* 1.3 62.3 + - - +
313C VAL* 4.1 12.1 - - - +
314C ARG* 3.4 23.2 + - - +
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Residues in contact with ASP 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B HIS* 2.6 27.2 + - - -
304B SER* 5.0 4.5 + - - -
307C ARG* 3.1 15.6 + - - +
308C THR* 3.8 14.4 - - - +
309C PHE 3.2 0.4 - - - -
310C ARG* 1.3 80.0 - - - +
312C SER* 1.3 57.4 + - - +
314C ARG* 2.5 38.3 + - - +
315C ALA* 2.9 28.2 + - - +
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B THR* 5.4 1.2 - - - +
308C THR 3.4 10.9 + - - -
309C PHE* 3.2 13.1 + - - -
311C ASP* 1.3 77.0 - - - +
313C VAL* 1.3 66.9 + - - +
315C ALA* 3.8 6.5 - - - +
316C ALA* 3.2 23.2 + - - +
337C ILE* 3.7 23.9 - - - +
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE* 3.7 30.3 - - + +
309C PHE* 3.2 44.0 + - + +
310C ARG* 4.5 12.8 - - - +
312C SER* 1.3 77.5 + - - +
314C ARG* 1.3 62.7 + - - +
316C ALA* 3.4 2.4 + - - +
317C SER* 3.1 26.3 + - - +
334C LEU* 4.1 19.5 - - + +
337C ILE* 3.9 17.5 - - + -
338C CYS* 4.9 1.8 - - - -
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Residues in contact with ARG 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 3.9 20.4 - - - -
301B HIS* 3.8 28.1 + - - -
302B TRP 5.0 4.0 + - - -
304B SER* 4.4 9.1 + - - -
305B ARG* 4.8 20.2 - - - +
310C ARG 3.4 16.2 + - - +
311C ASP* 2.5 36.5 + - - +
312C SER 3.3 0.6 - - - -
313C VAL* 1.3 81.2 - - - +
315C ALA* 1.3 57.1 + - - +
317C SER* 3.3 6.2 + - - +
318C GLU* 3.0 48.6 + - + +
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS* 4.5 7.4 - - + +
351B THR* 3.7 22.7 + - - +
311C ASP 2.9 17.5 + - - +
312C SER* 4.1 7.6 - - - +
313C VAL 3.3 0.2 - - - -
314C ARG* 1.3 78.2 - - - +
316C ALA* 1.3 57.6 + - - +
317C SER 3.4 0.2 - - - -
318C GLU* 3.9 12.4 + - - +
319C PHE* 3.4 22.2 + - - +
322C ARG* 5.6 0.9 + - - -
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B THR* 4.2 17.7 - - + -
312C SER 3.2 18.0 + - - +
313C VAL 3.7 3.1 - - - +
314C ARG 3.2 0.6 - - - -
315C ALA* 1.3 76.5 - - - +
317C SER* 1.3 60.2 + - - +
318C GLU 3.5 0.2 - - - -
319C PHE* 4.0 4.9 - - - -
320C ALA* 3.7 19.9 + - - +
330C GLN* 5.0 0.3 + - - -
333C MET* 4.0 21.8 - - + +
334C LEU* 4.7 8.5 - - + +
337C ILE* 3.7 22.0 - - + -
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Residues in contact with SER 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C VAL* 3.1 18.1 + - - +
314C ARG* 3.3 6.0 + - - -
316C ALA* 1.3 76.7 - - - +
318C GLU* 1.3 62.5 + - - +
319C PHE 3.3 1.1 - - - -
320C ALA 4.0 1.2 - - - +
321C SER* 3.3 23.9 + - - -
330C GLN* 4.6 11.4 + - - +
334C LEU* 3.8 23.2 - - - +
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Residues in contact with GLU 318 (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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305B ARG* 3.9 32.2 + - - -
345B GLY* 5.3 1.9 - - - -
346B LEU 5.7 0.3 + - - -
314C ARG* 3.0 43.8 + - + +
315C ALA* 4.1 11.4 - - - +
317C SER* 1.3 77.7 - - - +
319C PHE* 1.3 60.3 + - - +
321C SER* 4.1 3.2 - - - -
322C ARG* 3.3 48.1 + - + +
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Residues in contact with PHE 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN* 3.8 34.1 - - + -
351B THR* 4.9 6.7 - - + -
352B LEU* 3.6 28.3 - - + -
363B ILE* 3.9 37.0 - - + -
367B LEU* 4.8 1.8 - - + -
315C ALA 3.4 16.7 + - - +
316C ALA* 4.3 6.1 - - - +
317C SER 3.3 0.4 - - - -
318C GLU* 1.3 80.1 - - - +
320C ALA* 1.3 62.5 + - - +
321C SER 3.2 1.5 + - - -
322C ARG* 3.8 10.2 + - - +
323C ASN* 3.3 52.5 + - - +
325C LEU* 4.5 5.6 - - + -
333C MET* 4.2 17.3 - - + -
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ALA 3.7 13.4 + - - +
317C SER 3.8 1.7 + - - +
319C PHE* 1.3 78.6 - - - +
321C SER* 1.3 57.8 + - - +
323C ASN 4.5 0.7 - - - -
324C GLN* 4.3 0.5 - - - -
325C LEU* 3.5 48.7 + - + +
330C GLN* 3.4 43.5 + - + +
333C MET* 4.1 6.3 - - - -
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Residues in contact with SER 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 3.1 27.3 + - - -
317C SER 3.3 18.2 + - - -
318C GLU* 4.2 4.3 - - - -
319C PHE 3.2 0.6 - - - -
320C ALA* 1.3 78.1 - - - +
322C ARG* 1.3 64.2 + - - +
323C ASN 3.3 1.8 - - - -
324C GLN* 3.7 6.6 + - - +
330C GLN* 5.4 2.5 - - - -
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Residues in contact with ARG 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 4.2 25.3 - - + +
120A TYR* 3.6 18.5 + - - +
305B ARG* 5.1 2.4 - - - +
342B LYS 4.8 4.9 + - - -
343B THR* 3.0 24.0 + - - +
344B GLU 3.7 8.5 + - - -
345B GLY* 3.4 23.6 - - - +
348B GLN* 3.6 24.2 + - - +
315C ALA 5.6 0.8 + - - -
318C GLU* 3.3 36.1 + - + +
319C PHE* 3.8 18.1 + - - +
321C SER* 1.3 78.8 - - - +
323C ASN* 1.3 70.5 + - - +
324C GLN* 3.6 8.7 + - - +
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Residues in contact with ASN 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TYR* 4.6 2.8 - - - -
367B LEU* 3.4 44.2 - - + +
319C PHE* 3.3 45.8 + - - +
321C SER 3.3 0.4 - - - -
322C ARG* 1.3 89.9 + - - +
324C GLN* 1.3 71.5 + - - +
325C LEU* 3.4 7.7 + - + -
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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) + - + + + + + -
------------------------------------------------------------
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