Contacts of the helix formed by residues 301 - 315 (chain A) in PDB entry 2YTZ
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 ARG 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLN 5.8 1.8 + - - -
8A GLU* 5.2 1.8 - - - +
28A TYR* 5.9 0.2 + - - -
30A PRO* 3.5 29.7 + - - +
31A ARG* 4.8 8.2 - - - +
33A ALA* 3.7 26.0 - - + +
34A LEU* 4.2 17.3 - - + +
37A ASP* 2.8 12.3 + - - +
300A ALA* 1.3 103.6 + - - +
302A LYS* 1.3 52.8 + - - +
303A LYS* 3.4 29.8 - - - +
304A GLN* 3.4 16.6 + - - +
305A ALA* 2.8 33.8 + - - +
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Residues in contact with LYS 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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294A ALA 3.4 15.5 - - - +
295A GLU* 2.7 28.9 + - - +
297A LEU 2.8 28.8 + - - +
298A SER* 5.1 1.6 - - - -
299A LEU* 4.0 19.7 + - + +
300A ALA 3.8 1.2 - - - -
301A ARG* 1.3 72.6 - - - +
303A LYS* 1.3 70.3 + - + +
305A ALA* 3.5 5.8 - - - +
306A LEU* 2.8 51.1 + - + +
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Residues in contact with LYS 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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300A ALA 4.9 1.8 - - - -
301A ARG* 3.6 25.1 - - - +
302A LYS* 1.3 80.0 - - + +
304A GLN* 1.3 94.8 + - + +
306A LEU* 3.3 6.3 + - - +
307A LYS* 2.9 31.3 + - - +
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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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31A ARG* 3.0 39.4 + - - +
34A LEU* 3.7 22.1 - - + +
223A LYS* 5.0 6.7 + - - +
301A ARG* 3.4 18.5 + - - +
302A LYS 3.3 0.6 - - - -
303A LYS* 1.3 102.9 + - + +
305A ALA* 1.3 57.9 + - - +
307A LYS* 3.7 14.1 - - + +
308A LEU* 2.9 32.2 + - - +
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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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34A LEU* 3.5 17.2 - - + +
37A ASP* 4.4 3.4 - - + +
38A ILE* 4.2 12.6 - - + -
299A LEU* 3.7 26.2 - - + -
301A ARG 2.8 19.3 + - - +
302A LYS 3.5 4.5 - - - +
304A GLN* 1.3 77.6 - - - +
306A LEU* 1.3 57.1 + - - +
308A LEU* 4.0 1.7 - - - +
309A LEU* 3.0 38.0 + - + +
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Residues in contact with LEU 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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291A VAL* 4.0 4.9 - - + +
294A ALA* 3.8 22.4 - - + -
295A GLU* 3.3 33.7 - - + +
302A LYS* 2.8 52.5 + - + +
303A LYS* 3.7 5.8 - - - +
305A ALA* 1.3 70.6 - - + +
307A LYS* 1.3 61.4 + - - +
309A LEU* 4.0 2.9 - - + +
310A LYS* 2.9 57.1 + - - +
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Residues in contact with LYS 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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223A LYS* 5.1 11.1 - - - +
303A LYS 2.9 18.3 + - - +
304A GLN* 3.7 13.3 - - + +
306A LEU* 1.3 77.9 - - - +
308A LEU* 1.3 59.8 + - - +
310A LYS* 4.2 5.6 - - - +
311A MET* 3.3 22.3 + - - +
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Residues in contact with LEU 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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34A LEU* 4.7 10.8 - - + -
38A ILE* 4.6 16.8 - - + -
221A TYR* 3.8 33.7 - - + +
222A TYR 5.0 0.4 - - - +
223A LYS* 4.5 26.2 - - + +
304A GLN 2.9 18.3 + - - +
305A ALA 4.0 2.9 - - - +
307A LYS* 1.3 75.6 - - - +
309A LEU* 1.3 66.9 + - + +
311A MET* 3.3 4.4 + - + +
312A ILE* 3.1 40.1 + - + +
356A HIS* 4.2 21.1 - - + +
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Residues in contact with LEU 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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38A ILE* 4.0 26.0 - - + -
41A VAL* 4.4 9.9 - - + -
219A LEU* 4.8 7.0 - - + -
287A VAL* 4.2 9.0 - - + +
290A MET* 4.0 38.1 - - + +
291A VAL* 3.9 15.6 - - + +
294A ALA* 3.8 28.3 - - + -
305A ALA* 3.0 23.3 + - + +
306A LEU* 4.0 4.3 - - - +
308A LEU* 1.3 78.7 - - + +
310A LYS* 1.3 56.8 + - - +
312A ILE* 3.5 9.7 + - + +
313A ASP* 2.9 30.1 + - - +
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Residues in contact with LYS 310 (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* 3.7 19.1 - - + +
295A GLU* 3.0 26.4 + - - -
306A LEU* 2.9 48.6 + - + +
307A LYS* 4.2 5.6 - - - +
309A LEU* 1.3 73.6 - - - +
311A MET* 1.3 66.7 + - - +
313A ASP* 3.1 8.4 + - + +
314A GLN* 3.0 27.2 + - - +
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Residues in contact with MET 311 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A LYS 3.3 13.1 + - - +
308A LEU* 3.3 10.7 + - + +
310A LYS* 1.3 79.7 - - - +
312A ILE* 1.3 63.9 + - - +
314A GLN* 3.0 43.9 - - - +
315A GLU* 3.1 9.2 + - - +
354A ARG* 3.8 42.8 - - + +
355A THR 4.1 9.2 - - - +
356A HIS* 3.6 29.2 - - + +
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.8 28.7 - - + -
220A ALA 5.8 1.1 - - - +
221A TYR* 3.6 35.0 - - + -
282A LYS* 2.8 44.1 + - + -
287A VAL* 4.2 7.0 - - + -
308A LEU* 3.1 32.3 + - + +
309A LEU* 3.9 8.7 - - + +
311A MET* 1.3 75.7 - - - +
313A ASP* 1.3 52.2 + - - +
315A GLU* 3.3 15.7 + - + +
356A HIS* 3.4 24.2 - - + +
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Residues in contact with ASP 313 (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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282A LYS* 3.2 6.1 + - - -
284A GLU* 2.7 35.0 - - - +
287A VAL* 3.9 8.3 - - + +
288A SER* 2.8 36.6 + - - -
291A VAL* 3.8 22.1 - - + +
309A LEU 2.9 19.2 + - - +
310A LYS* 3.1 7.7 + - - +
312A ILE* 1.3 77.8 - - - +
314A GLN* 1.3 58.1 + - - +
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Residues in contact with GLN 314 (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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310A LYS 3.0 19.3 + - - +
311A MET* 3.0 28.7 - - - +
313A ASP* 1.3 76.4 - - - +
315A GLU* 1.3 75.2 + - - +
316A LEU* 5.5 0.7 - - - +
346A ARG* 4.9 6.1 - - - +
353A THR* 3.5 27.7 - - - +
354A ARG* 3.4 20.6 - - - +
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Residues in contact with GLU 315 (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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281A LEU* 6.0 0.3 - - - +
282A LYS* 2.9 24.0 + - + +
311A MET* 3.1 13.5 + - - +
312A ILE* 3.3 12.1 + - - +
314A GLN* 1.3 88.0 + - - +
316A LEU* 1.3 75.0 + - - +
317A ASP 3.6 0.7 + - - -
353A THR* 3.7 1.8 - - - -
354A ARG 3.5 11.0 - - - +
355A THR* 3.2 19.8 + - - -
356A HIS* 2.7 49.4 + - - +
357A PHE* 4.0 5.0 - - - -
363A LYS* 3.3 17.2 - - + -
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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