Contacts of the helix formed by residues 296 - 310 (chain A) in PDB entry 2W3C
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 PRO 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ASN* 3.7 35.4 - - + +
294A THR 4.4 1.8 - - - +
295A ASN* 1.4 89.4 - - + +
297A PRO* 1.4 76.2 - - + +
298A GLY* 3.3 1.8 - - - +
299A ALA* 3.1 29.4 + - + +
300A THR* 3.5 1.4 + - - -
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Residues in contact with PRO 297 (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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295A ASN 3.3 5.6 - - - +
296A PRO* 1.4 83.6 - - + +
298A GLY* 1.3 58.0 + - - +
299A ALA 3.3 0.3 + - - -
300A THR* 3.4 7.7 + - - -
301A SER* 3.1 30.1 + - - -
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Residues in contact with GLY 298 (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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296A PRO* 3.3 2.0 - - - +
297A PRO* 1.3 79.5 - - - +
299A ALA* 1.3 60.2 + - - +
301A SER* 3.8 10.7 - - - -
302A SER* 2.8 27.9 + - - -
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Residues in contact with ALA 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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244A ASN* 5.9 2.5 - - + +
247A GLN* 5.3 6.1 - - + +
248A ASN* 6.2 4.0 - - + +
251A LYS* 6.1 0.7 - - - +
290A LEU 4.5 1.6 - - - +
295A ASN* 4.3 14.4 - - + +
296A PRO* 3.1 25.3 + - + +
298A GLY* 1.3 77.1 - - - +
300A THR* 1.3 63.1 + - - +
302A SER* 3.4 5.5 + - - -
303A CYS* 3.3 31.4 + - - -
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Residues in contact with THR 300 (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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290A LEU 4.0 7.4 - - - -
291A VAL* 3.4 29.5 - - - +
292A SER 3.0 24.0 + - - +
293A PRO* 4.9 2.6 - - + +
295A ASN* 3.3 12.5 + - - +
296A PRO 3.5 1.9 + - - -
297A PRO* 3.4 9.3 + - - -
299A ALA* 1.3 75.1 - - - +
301A SER* 1.3 66.7 + - - +
303A CYS* 3.3 3.3 + - - +
304A GLN* 2.9 43.3 + - - +
342A ARG 5.4 0.7 - - - +
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO 3.1 20.2 + - - -
298A GLY* 3.8 11.2 - - - -
300A THR* 1.3 76.3 - - - +
302A SER* 1.3 57.4 + - - -
304A GLN* 3.3 15.6 + - - +
305A LYS* 3.0 43.7 + - - +
344A CYS* 5.1 1.8 - - - -
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LYS* 3.2 36.8 + - - +
298A GLY 2.8 20.1 + - - -
299A ALA* 3.4 8.7 + - - -
300A THR 3.3 0.2 - - - -
301A SER* 1.3 77.5 - - - +
303A CYS* 1.3 60.1 + - - +
305A LYS* 3.6 10.8 + - - +
306A ALA* 3.0 26.7 + - - +
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Residues in contact with CYS 303 (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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247A GLN* 5.0 4.9 - - - -
251A LYS* 4.1 17.0 - - - -
256A ILE* 4.1 25.7 - - + +
290A LEU* 3.5 39.0 - - + +
291A VAL* 3.9 7.9 - - + -
299A ALA* 3.3 17.6 + - - +
300A THR 3.3 3.2 + - - +
302A SER* 1.3 75.0 - - - +
304A GLN* 1.3 54.9 + - - +
306A ALA* 3.2 1.9 + - - +
307A MET* 2.7 42.4 + - + +
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Residues in contact with GLN 304 (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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291A VAL* 3.8 14.3 - - + +
300A THR* 2.9 26.6 + - - +
301A SER* 3.3 21.2 + - - +
303A CYS* 1.3 75.8 - - - +
305A LYS* 1.3 57.4 + - - +
307A MET* 3.5 5.9 + - - +
308A PHE 3.1 16.8 + - - -
339A GLU 2.8 23.2 + - - -
340A VAL 3.1 24.2 + - - +
342A ARG* 3.0 26.2 + - - +
343A GLY 4.7 1.7 - - - +
344A CYS* 3.6 19.8 + - - +
347A ASN* 2.9 23.6 + - - +
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Residues in contact with LYS 305 (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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301A SER* 3.0 31.4 + - - +
302A SER* 3.8 9.2 - - - +
303A CYS 3.3 0.2 - - - -
304A GLN* 1.3 72.3 - - - +
306A ALA* 1.3 56.2 + - - +
308A PHE* 3.3 6.3 + - - +
309A GLN* 2.8 48.7 + - + +
344A CYS* 4.9 15.0 - - - -
346A VAL* 6.2 7.2 - - + -
347A ASN* 5.1 1.1 - - - -
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Residues in contact with ALA 306 (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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251A LYS* 4.8 6.3 - - + -
256A ILE* 3.8 23.8 - - + -
302A SER 3.0 19.4 + - - +
303A CYS 3.5 4.7 - - - +
305A LYS* 1.3 76.4 - - - +
307A MET* 1.3 57.0 + - - +
309A GLN* 3.9 7.0 - - - +
310A CYS* 3.0 36.7 + - - +
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Residues in contact with MET 307 (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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256A ILE* 3.9 8.7 - - + -
287A VAL* 3.6 40.2 - - + +
290A LEU* 4.0 24.0 - - + -
291A VAL* 3.8 30.7 - - + -
303A CYS* 2.7 20.6 + - + +
304A GLN 3.7 5.6 - - - +
306A ALA* 1.3 69.1 - - - +
308A PHE* 1.3 63.2 + - - +
310A CYS* 4.1 5.2 - - - -
311A GLY 3.7 0.3 + - - -
312A LEU* 2.9 53.2 + - + -
313A LEU* 3.1 9.3 + - - +
340A VAL* 3.9 21.5 - - + -
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Residues in contact with PHE 308 (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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304A GLN 3.1 7.3 + - - +
305A LYS* 3.5 8.1 - - - +
307A MET* 1.3 74.2 - - - +
309A GLN* 1.3 92.2 + - - +
311A GLY 3.0 13.0 + - - -
313A LEU* 4.0 14.5 - - + +
314A GLN* 3.4 39.2 + - - +
346A VAL* 3.7 27.1 - - + -
347A ASN* 3.1 28.0 - - - +
350A TYR* 3.9 22.0 - + + -
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Residues in contact with GLN 309 (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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305A LYS* 2.8 31.0 + - + +
306A ALA* 3.3 8.0 + - - +
308A PHE* 1.3 98.9 - - - +
310A CYS* 1.3 57.6 + - + +
311A GLY 3.7 0.7 + - - -
346A VAL* 5.5 1.2 - - - +
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Residues in contact with CYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 4.1 5.8 - - - -
257A GLN* 3.8 42.1 - - + +
260A LYS* 3.1 24.7 - - - +
306A ALA 3.0 27.8 + - - +
307A MET* 4.0 8.1 - - - -
309A GLN* 1.3 77.0 - - + +
311A GLY* 1.3 56.4 + - - +
312A LEU* 4.0 14.6 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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