Contacts of the helix formed by residues 294 - 307 (chain A) in PDB entry 2XTJ
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 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A VAL* 4.0 12.8 - - - +
292A GLY 3.0 7.5 + - - -
293A TYR* 1.3 77.7 - - - +
295A ARG* 1.3 57.7 + - - +
296A VAL* 3.6 1.7 - - - +
297A LEU* 3.1 28.9 + - - +
298A ASN* 2.9 33.0 + - - +
326A SER* 2.7 13.3 + - - -
144P GLU* 2.6 27.6 + - - -
147P SER* 5.4 1.3 - - - -
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR* 4.0 45.0 + - - +
294A SER* 1.3 71.1 + - - +
296A VAL* 1.3 56.2 + - - +
298A ASN* 3.9 3.9 - - - +
299A ALA* 3.1 26.5 + - - +
65P HIS* 3.5 56.3 + - + +
66P ARG 5.5 2.8 + - - -
142P TYR* 4.1 21.4 + - + -
144P GLU* 3.4 10.6 + - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 4.0 13.7 - - + -
265A LEU* 3.7 18.8 - - + +
294A SER* 3.6 9.4 - - - +
295A ARG* 1.3 76.5 - - - +
297A LEU* 1.3 69.9 + - - +
299A ALA* 3.2 3.3 + - - +
300A ALA 3.0 18.7 + - - -
79P VAL* 4.2 12.8 - - + -
81P VAL* 3.7 23.6 - - + -
119P LEU* 3.5 24.1 - - + +
142P TYR* 3.7 12.8 - - + +
144P GLU* 3.3 23.0 + - + +
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Residues in contact with LEU 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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261A VAL* 4.4 24.2 - - + +
264A THR* 3.8 30.1 - - + -
265A LEU* 4.2 11.2 - - + -
268A LEU* 3.9 16.4 - - + -
289A LEU* 5.2 0.2 - - + -
294A SER* 3.1 20.6 + - - +
296A VAL* 1.3 77.8 - - - +
298A ASN* 1.3 64.2 + - - +
299A ALA 3.0 1.6 + - - -
300A ALA* 3.0 12.3 + - - +
301A CYS* 3.1 19.2 + - - -
326A SER* 4.0 16.4 - - - +
327A PRO* 3.9 35.2 - - + -
149P VAL* 4.5 10.1 - - + -
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Residues in contact with ASN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR* 3.6 14.5 - - + +
294A SER 2.9 16.7 + - - +
295A ARG* 3.9 6.3 - - - +
297A LEU* 1.3 72.8 - - - +
299A ALA* 1.3 56.2 + - - +
301A CYS* 3.6 5.8 + - - +
302A GLN* 3.0 26.7 + - - +
326A SER* 2.7 28.1 + - - -
327A PRO* 4.1 3.1 - - - +
329A SER* 2.9 25.2 + - - -
330A ALA* 3.4 31.0 - - + +
331A PRO* 5.1 2.2 - - + +
332A GLU* 3.9 6.1 - - - +
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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
----------------------------------------------------------
295A ARG 3.1 19.1 + - - +
296A VAL* 3.4 9.0 - - - +
297A LEU 3.1 0.4 - - - -
298A ASN* 1.3 74.0 - - - +
300A ALA* 1.3 61.8 + - - +
301A CYS 3.2 0.2 - - - -
302A GLN* 3.1 14.2 + - - +
303A ARG* 2.8 31.1 + - - +
118P LEU 5.4 0.2 - - - -
119P LEU* 4.4 11.2 - - + -
142P TYR* 4.6 6.7 - - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 3.7 26.7 - - + -
268A LEU* 3.8 10.5 - - + -
296A VAL 3.0 5.6 + - - +
297A LEU 3.0 8.0 + - - +
299A ALA* 1.3 75.7 - - - +
301A CYS* 1.3 58.4 + - - +
303A ARG* 3.2 5.2 + - - +
304A LEU* 2.9 30.0 + - - +
118P LEU* 3.8 30.1 - - + +
119P LEU* 4.2 8.9 - - + +
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Residues in contact with CYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.3 16.6 - - - -
287A LEU* 4.6 10.5 - - - -
297A LEU* 3.1 17.8 + - - -
298A ASN* 3.6 11.4 - - - +
300A ALA* 1.3 74.8 - - - +
302A GLN* 1.3 63.9 + - - +
304A LEU* 3.2 2.3 + - - -
305A ALA* 2.9 21.5 + - - +
311A LEU* 3.3 17.1 - - + +
327A PRO* 4.2 21.3 - - - -
330A ALA* 4.6 2.2 - - + -
332A GLU* 4.5 2.5 - - - -
333A VAL* 3.3 31.9 - - + -
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Residues in contact with GLN 302 (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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298A ASN 3.0 12.7 + - - +
299A ALA* 3.1 14.7 + - - +
301A CYS* 1.3 76.0 - - - +
303A ARG* 1.3 61.9 + - - +
305A ALA* 3.3 3.1 + - - +
306A ARG* 3.1 51.1 + - + +
332A GLU* 3.1 41.9 - - + +
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Residues in contact with ARG 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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272A ARG* 3.2 33.7 - - - +
299A ALA 2.8 17.7 + - - +
300A ALA 3.7 3.8 - - - +
302A GLN* 1.3 75.0 - - - +
304A LEU* 1.3 61.4 + - - +
306A ARG* 3.4 41.0 + - - +
307A ALA* 3.5 14.6 + - - +
117P GLY 4.3 7.2 + - - -
118P LEU* 3.2 42.0 - - + +
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Residues in contact with LEU 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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268A LEU* 3.7 28.5 - - + +
271A ILE* 4.9 4.5 - - + -
272A ARG* 3.8 42.0 - - + +
275A GLN* 4.8 0.4 - - - +
285A VAL* 4.7 5.8 - - + -
300A ALA 2.9 16.4 + - - +
301A CYS* 3.7 3.6 - - - +
302A GLN 3.2 0.2 - - - -
303A ARG* 1.3 75.9 - - - +
305A ALA* 1.3 64.4 + - - +
307A ALA* 3.3 10.7 + - + +
309A VAL* 3.3 45.1 + - + +
311A LEU* 3.7 27.6 - - + -
118P LEU* 3.8 9.4 - - + -
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Residues in contact with ALA 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 CYS 2.9 17.0 + - - +
302A GLN 3.3 5.4 + - - +
304A LEU* 1.3 75.3 - - - +
306A ARG* 1.3 55.3 + - - +
308A GLY* 2.7 26.5 + - - -
309A VAL 3.8 13.2 - - - +
311A LEU* 4.0 3.3 - - + +
332A GLU* 3.6 34.1 - - + +
408A LEU* 3.4 18.0 - - + +
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLN* 3.1 45.9 + - + +
303A ARG* 3.5 34.7 + - - +
304A LEU 3.3 0.2 - - - -
305A ALA* 1.3 74.7 - - - +
307A ALA* 1.3 56.5 + - - +
308A GLY* 3.1 3.7 + - - -
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.7 34.3 - - - +
275A GLN* 3.3 25.1 + - - +
303A ARG* 3.5 13.4 + - - +
304A LEU* 3.3 11.8 + - - +
305A ALA 3.1 1.4 - - - -
306A ARG* 1.3 76.7 - - - +
308A GLY* 1.3 57.5 - - - +
309A VAL 3.5 1.1 - - - -
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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