Contacts of the helix formed by residues 295 - 314 (chain A) in PDB entry 3C98
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 HIS 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 3.7 26.0 - - + +
248A THR* 4.3 10.3 - - + +
293A HIS 3.7 1.4 + - - -
294A LYS* 1.3 76.6 - - - +
296A ILE* 1.3 91.0 + - + +
297A ALA* 3.1 20.4 + - + +
298A GLU* 3.1 24.6 + - + +
299A VAL* 3.2 9.9 + - - +
473A TYR* 3.5 46.6 - + + +
475A LEU* 6.0 0.2 - - - +
476A SER* 3.0 29.5 + - - -
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 3.0 28.5 + - + +
249A PHE* 4.2 22.2 - - + +
252A MET* 3.6 24.2 - - + -
294A LYS 3.7 0.6 + - - -
295A HIS* 1.3 85.7 + - + +
297A ALA* 1.3 65.0 + - + +
298A GLU 3.1 1.8 + - - -
299A VAL* 3.5 18.4 + - + +
300A SER* 4.4 4.9 + - - -
351A ALA* 4.5 12.6 - - + +
354A CYS* 4.0 20.2 - - + -
355A MET* 4.0 28.9 - - + +
358A TYR* 6.4 0.9 - - + -
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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
----------------------------------------------------------
295A HIS* 3.1 21.4 + - + +
296A ILE* 1.3 81.9 - - + +
298A GLU* 1.3 58.5 + - - +
300A SER* 5.3 0.7 - - - -
301A GLN* 5.1 5.5 + - - +
355A MET* 6.2 0.9 - - - -
473A TYR* 4.0 24.2 + - + +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS* 3.5 28.4 - - - +
295A HIS* 3.1 15.5 + - + +
296A ILE 3.1 0.4 - - - -
297A ALA* 1.3 78.6 - - - +
299A VAL* 1.3 61.0 + - - +
300A SER 3.5 2.0 - - - -
301A GLN* 3.3 12.9 + - - +
302A GLU* 2.9 30.3 + - + +
473A TYR* 3.2 38.0 + - + +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 4.0 43.5 - - + -
291A LEU* 4.5 15.0 - - + +
294A LYS* 4.1 11.9 - - + +
295A HIS 3.2 18.8 - - - +
296A ILE* 3.5 19.1 + - + +
298A GLU* 1.3 77.0 - - - +
300A SER* 1.3 63.7 + - - +
302A GLU* 3.1 15.5 + - - +
303A VAL* 3.1 19.0 + - + +
347A HIS 4.9 0.4 - - - +
351A ALA* 3.9 20.6 - - + -
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE 4.4 4.8 + - - -
297A ALA 5.3 0.8 - - - -
298A GLU 3.5 0.2 - - - -
299A VAL* 1.3 80.1 - - - +
301A GLN* 1.3 62.4 + - - +
303A VAL* 3.2 25.1 - - - +
304A THR* 3.2 15.9 - - - +
348A LEU* 5.0 5.3 - - - +
351A ALA* 4.6 15.2 - - - +
355A MET* 6.6 0.2 - - - -
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Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA 5.1 3.6 + - - +
298A GLU* 3.3 15.7 + - - +
299A VAL 3.3 0.2 - - - -
300A SER* 1.3 79.1 - - - +
302A GLU* 1.3 70.8 + - - +
304A THR* 3.3 16.0 + - - +
305A ARG* 3.3 25.2 + - - +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA* 5.9 0.4 - - + +
291A LEU* 3.7 17.3 - - + -
294A LYS* 3.5 27.3 + - - +
298A GLU 2.9 17.7 + - - +
299A VAL 3.1 5.8 + - - +
301A GLN* 1.3 85.5 - - - +
303A VAL* 1.3 64.5 + - - +
305A ARG* 2.9 35.7 + - - +
306A SER* 3.3 22.7 + - - -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 5.1 6.1 - - + -
291A LEU* 3.4 33.7 - - + -
299A VAL* 3.1 13.6 + - + +
300A SER* 3.2 16.8 - - - +
302A GLU* 1.3 75.3 - - - +
304A THR* 1.3 59.4 + - - +
306A SER* 3.2 7.3 + - - -
307A LEU* 2.8 34.4 + - - +
344A TYR* 3.9 14.2 - - + +
347A HIS* 4.3 15.3 - - + +
348A LEU* 3.4 35.7 - - + -
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER* 3.2 18.5 + - - +
301A GLN* 3.3 14.1 + - - +
303A VAL* 1.3 78.2 - - + +
305A ARG* 1.3 68.6 + - - +
306A SER 3.0 1.8 - - - -
307A LEU* 3.1 18.3 + - + +
308A LYS* 3.1 22.1 + - - +
325A ARG* 3.9 36.6 - - + +
348A LEU* 4.1 13.7 - - + -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 3.3 31.7 + - - +
302A GLU* 2.9 37.5 + - - +
303A VAL 3.3 0.2 - - - -
304A THR* 1.3 81.8 + - - +
306A SER* 1.3 63.1 + - - +
308A LYS* 4.3 18.5 - - - +
309A ASP* 3.5 18.7 + - - +
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Residues in contact with SER 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.7 8.3 - - - +
302A GLU* 3.3 19.6 + - - -
303A VAL* 3.2 10.5 + - - -
304A THR 3.0 0.6 - - - -
305A ARG* 1.3 82.5 - - - +
307A LEU* 1.3 62.4 + - - +
309A ASP* 3.8 7.2 - - - +
310A PHE* 3.2 22.2 + - - +
344A TYR* 3.0 20.8 + - - -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL 2.8 16.2 + - - +
304A THR* 3.1 10.5 + - + +
306A SER* 1.3 75.7 - - - +
308A LYS* 1.3 55.0 + - - +
310A PHE* 2.9 9.7 + - + +
311A SER* 2.6 40.7 + - - -
324A MET 4.4 15.5 - - - +
325A ARG* 5.0 5.6 - - + -
328A SER* 4.4 24.2 - - - +
330A MET* 5.2 8.3 - - + -
341A LEU* 4.7 13.7 - - + -
344A TYR* 3.8 37.7 - - + -
348A LEU* 4.4 18.8 - - + -
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR 3.1 15.7 + - - +
305A ARG* 4.3 20.2 - - - +
307A LEU* 1.3 81.1 - - - +
309A ASP* 1.3 59.9 + - + +
311A SER* 3.7 9.0 - - - -
312A SER* 3.0 30.1 + - - -
324A MET 5.1 9.2 - - - +
325A ARG* 6.4 2.7 - - + -
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 3.5 19.7 + - - +
306A SER* 3.8 7.6 + - - +
308A LYS* 1.3 83.6 - - + +
310A PHE* 1.3 64.1 + - - +
312A SER* 3.0 20.4 + - - -
313A SER* 3.2 12.6 + - - -
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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
----------------------------------------------------------
306A SER 3.2 12.2 + - - +
307A LEU* 2.9 11.9 + - + +
309A ASP* 1.3 83.8 + - - +
311A SER* 1.3 68.1 + - - +
313A SER* 3.1 17.7 + - - -
314A LYS* 3.3 38.1 + - + +
316A MET* 4.9 4.5 - - - -
337A TYR* 4.2 19.1 - + + -
340A GLU* 3.7 34.5 - - + -
341A LEU* 3.8 28.0 - - + -
344A TYR* 3.9 22.7 - + - +
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 2.6 22.4 + - - -
308A LYS* 3.7 11.0 - - - -
310A PHE* 1.3 79.8 - - - +
312A SER* 1.3 62.7 + - - +
314A LYS 3.2 2.4 + - - -
315A ARG 3.2 15.4 + - - -
316A MET* 3.3 44.1 + - - +
324A MET 5.8 0.5 + - - -
330A MET* 4.3 18.0 - - - +
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LYS 3.0 15.1 + - - -
309A ASP* 3.0 20.3 + - - -
311A SER* 1.3 72.6 + - - +
313A SER* 1.3 60.5 + - - +
314A LYS 3.0 4.9 - - - -
315A ARG* 3.1 18.6 + - - +
316A MET 5.7 0.7 - - - -
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ASP* 3.2 12.8 + - - -
310A PHE* 3.1 14.9 + - - -
312A SER* 1.3 81.6 + - - +
314A LYS* 1.3 71.8 + - - +
315A ARG* 4.6 11.9 + - - -
139B SER* 5.2 1.9 + - - -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 3.3 39.0 + - + +
311A SER 3.2 7.4 + - - +
312A SER 3.0 0.8 - - - -
313A SER* 1.3 89.7 + - - +
315A ARG* 1.3 74.6 + - - +
316A MET* 2.9 28.3 + - + -
334A MET* 3.9 13.0 - - - +
337A TYR* 3.3 47.8 + - + +
136B ALA* 5.6 6.7 - - - +
139B SER* 3.9 17.9 + - - +
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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