Contacts of the helix formed by residues 307 - 318 (chain A) in PDB entry 2ATW
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 GLY 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.1 12.5 - - - +
304A GLY 2.7 20.0 + - - -
306A GLU* 1.3 72.1 - - - +
308A GLN* 1.3 56.5 + - - +
309A ASN 3.5 0.2 + - - -
310A ALA* 3.5 0.9 + - - +
311A ARG* 2.9 34.2 + - - +
7B A 3.8 3.0 - - - -
8B A 3.3 27.5 + - - -
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Residues in contact with GLN 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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213A GLU* 3.8 19.5 + - - +
216A HIS* 3.6 29.3 - - - +
217A ARG* 3.0 47.6 + - - +
303A ILE 3.4 1.8 + - - -
304A GLY 3.7 0.4 + - - -
305A LYS* 2.9 20.6 + - + +
306A GLU 3.4 0.6 - - - -
307A GLY* 1.3 77.0 - - - +
309A ASN* 1.3 57.7 + - - +
311A ARG* 3.8 13.0 - - - +
312A LEU* 2.9 37.8 + - + +
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Residues in contact with ASN 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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217A ARG* 5.4 3.1 - - - +
219A LYS* 2.7 34.8 + - - +
256A ASP* 3.9 3.6 - - - +
272A LEU* 2.7 30.8 + - - +
273A SER 3.6 2.8 - - - +
274A PRO* 4.1 6.7 - - - +
275A ALA* 4.2 1.8 - - - +
301A LEU* 3.6 17.9 + - - +
302A ALA* 3.0 24.6 + - - +
303A ILE 3.2 5.8 + - - +
304A GLY* 4.1 4.6 - - - +
308A GLN* 1.3 79.5 + - - +
310A ALA* 1.3 58.9 + - - +
312A LEU* 3.5 0.6 + - - -
313A ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 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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272A LEU* 4.0 11.2 - - + -
302A ALA 3.6 1.0 + - - -
303A ILE* 3.2 13.2 + - + +
307A GLY 4.1 2.2 - - - +
309A ASN* 1.3 80.4 - - - +
311A ARG* 1.3 57.1 + - - +
313A ALA* 3.4 2.1 + - - +
314A ALA* 2.9 31.2 + - - +
321A ILE* 4.3 3.4 - - + +
323A ILE* 3.8 20.2 - - + -
8B A 3.7 26.2 - - - +
10B A 3.9 10.1 + - - +
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Residues in contact with ARG 311 (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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213A GLU* 2.8 43.0 + - - +
305A LYS 4.9 0.6 + - - -
306A GLU* 3.1 29.3 + - - +
307A GLY* 2.9 20.2 + - - +
308A GLN* 3.8 18.9 - - - +
310A ALA* 1.3 77.2 - - - +
312A LEU* 1.3 62.4 + - - +
314A ALA* 3.3 1.9 + - - +
315A ARG* 3.0 31.1 + - - +
8B A 4.6 7.1 + - - -
10B A 3.4 42.9 + - + +
11B G 5.2 11.3 - - - -
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Residues in contact with LEU 312 (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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211A ALA* 3.4 37.6 - - + +
212A ARG 3.9 6.3 - - - +
213A GLU* 4.2 13.7 - - + +
217A ARG* 3.6 43.5 - - + +
219A LYS* 3.8 22.0 - - + -
308A GLN* 2.9 35.0 + - + +
311A ARG* 1.3 76.5 - - - +
313A ALA* 1.3 57.7 + - - +
315A ARG* 3.4 19.6 + - - +
316A LEU* 2.8 30.7 + - - +
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Residues in contact with ALA 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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219A LYS* 3.8 4.1 - - - +
271A ALA* 3.7 28.7 - - + -
272A LEU* 3.7 15.7 - - + -
309A ASN 3.0 18.1 + - - +
310A ALA 3.7 1.1 - - - +
312A LEU* 1.3 76.2 - - - +
314A ALA* 1.3 58.5 + - - +
316A LEU* 3.1 2.9 + - - +
317A THR* 2.9 36.6 + - - +
321A ILE* 3.6 20.0 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.2 + - - +
311A ARG 3.5 4.7 - - - +
313A ALA* 1.3 76.9 - - - +
315A ARG* 1.3 58.1 + - - +
317A THR* 4.0 0.4 - - - -
318A GLY* 2.8 29.8 + - - -
319A TRP 3.4 23.6 + - - +
321A ILE* 3.7 5.4 - - + +
10B A 3.7 34.3 - - + +
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Residues in contact with ARG 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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186A PRO* 5.5 7.5 - - - +
210A VAL 4.5 3.5 + - - +
211A ALA* 3.9 13.4 - - + +
212A ARG* 2.9 47.7 + - - +
213A GLU* 4.1 9.0 + - - +
311A ARG* 3.0 27.9 + - - +
312A LEU* 3.7 13.9 - - - +
314A ALA* 1.3 76.9 - - - +
316A LEU* 1.3 66.1 + - - +
317A THR 3.4 0.3 + - - -
318A GLY* 3.6 6.9 + - - -
10B A 3.5 23.6 - - - +
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Residues in contact with LEU 316 (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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209A ALA* 3.5 53.0 - - + +
210A VAL 3.8 1.3 - - - +
211A ALA* 3.7 11.2 - - + +
219A LYS* 3.5 26.5 - - + +
221A ALA* 3.9 15.0 - - + +
258A ILE* 3.9 34.1 - - + -
267A PHE* 3.9 9.8 - - + -
271A ALA* 4.0 15.9 - - + -
312A LEU 2.8 19.7 + - - +
313A ALA* 3.1 6.0 + - - +
315A ARG* 1.3 80.0 - - - +
317A THR* 1.3 57.7 + - + +
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Residues in contact with THR 317 (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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267A PHE* 3.7 36.8 - - + -
268A VAL* 4.1 15.2 - - - +
271A ALA* 3.6 24.7 - - + -
288A ARG* 2.8 19.6 + - - -
313A ALA* 2.9 18.6 + - + +
314A ALA* 3.6 1.4 + - - -
316A LEU* 1.3 77.8 - - - +
318A GLY* 1.3 57.1 + - - +
319A TRP* 3.0 36.1 + - - +
321A ILE* 4.4 1.3 - - + +
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Residues in contact with GLY 318 (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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288A ARG* 3.3 30.0 + - - +
314A ALA 2.8 12.2 + - - -
315A ARG* 3.6 7.2 + - - -
317A THR* 1.3 78.8 - - - +
319A TRP* 1.3 58.3 + - - +
320A ARG* 4.3 0.7 + - - +
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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
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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