Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 4OWT
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 THR 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 6.5 2.0 - - + -
169A LYS* 3.5 17.9 - - - +
170A GLN* 4.3 9.0 - - - +
171A ILE 4.6 0.4 - - - +
172A ALA* 3.9 33.0 - - + -
304A ARG 4.2 0.4 + - - -
305A LEU* 1.3 78.4 - - - +
307A PRO* 1.3 76.7 - - + +
308A ASP* 3.8 4.2 + - - +
309A MSE 3.1 34.7 + - + +
310A GLU* 3.1 17.5 + - - +
336A TYR* 4.2 5.4 + - + -
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Residues in contact with PRO 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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131A MSE 3.4 49.8 - - + +
169A LYS* 4.0 12.3 - - + +
170A GLN* 3.2 36.8 - - - +
306A THR* 1.3 87.1 - - - +
308A ASP* 1.3 57.2 + - - +
310A GLU* 3.3 6.8 + - + +
311A THR* 3.0 35.2 + - - +
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Residues in contact with ASP 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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135A LEU* 4.4 17.9 - - + -
306A THR* 3.3 4.5 + - - +
307A PRO* 1.3 80.0 - - - +
309A MSE 1.3 62.0 + - - +
311A THR* 3.8 6.6 - - - +
312A LYS* 2.8 63.3 + - - +
335A GLN* 3.6 4.0 + - - -
336A TYR* 2.3 33.3 + - - +
97B GLU* 4.6 4.8 - - - +
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Residues in contact with MSE 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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172A ALA* 4.0 17.3 - - + -
173A GLY 4.4 2.9 - - - +
304A ARG 4.7 0.7 - - - +
305A LEU* 4.0 18.2 - - + -
306A THR* 3.1 45.8 + - + +
308A ASP* 1.3 77.0 - - - +
310A GLU* 1.3 65.0 + - - +
312A LYS* 3.9 1.2 - - - +
313A LEU* 3.0 27.5 + - - +
332A PHE* 4.1 14.9 - - + -
336A TYR* 3.7 41.3 - - + -
345A LEU* 3.9 38.6 - - + -
349A LEU* 4.5 4.5 - - + -
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Residues in contact with GLU 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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131A MSE 5.4 1.7 - - - +
169A LYS* 2.7 33.8 + - - -
302A ALA* 4.3 8.4 - - - +
305A LEU* 3.9 18.1 - - + +
306A THR 3.1 6.0 + - - +
307A PRO* 3.6 8.4 - - + +
309A MSE 1.3 78.0 - - - +
311A THR* 1.3 55.4 + - - +
313A LEU* 3.2 2.8 + - - +
314A LEU* 2.8 48.7 + - + +
352A TYR* 2.6 42.3 + - + +
356A VAL* 5.4 0.9 - - - +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PRO* 3.0 19.6 + - - +
308A ASP* 3.8 8.9 - - - +
309A MSE 3.3 0.2 - - - -
310A GLU* 1.3 75.9 - - - +
312A LYS* 1.3 58.6 + - + +
314A LEU* 3.6 8.1 + - - +
315A PHE* 3.0 27.7 + - - +
99B CYS* 3.7 21.1 - - - -
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Residues in contact with LYS 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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308A ASP* 2.8 43.1 + - - +
309A MSE 4.0 2.5 - - - +
311A THR* 1.3 78.7 - - + +
313A LEU* 1.3 60.0 + - - +
315A PHE* 3.4 1.4 + - - +
316A MSE 3.0 33.8 + - - +
332A PHE* 4.1 17.0 - - + -
335A GLN* 2.6 29.9 + - - -
336A TYR* 4.5 3.4 - - + -
97B GLU* 3.0 23.2 + - - -
98B PHE* 3.5 61.1 - - + -
99B CYS* 4.5 4.5 - - - -
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Residues in contact with LEU 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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305A LEU* 3.7 28.0 - - + -
309A MSE 3.0 15.6 + - - +
310A GLU* 3.8 3.4 - - - +
312A LYS* 1.3 73.2 - - - +
314A LEU* 1.3 64.9 + - - +
316A MSE 3.3 20.1 + - - +
317A THR* 2.9 31.7 + - - +
332A PHE* 4.2 14.6 - - + -
349A LEU* 3.8 23.8 - - + -
352A TYR* 4.1 10.3 - - + -
353A ILE* 4.0 30.1 - - + -
357A VAL* 6.0 0.4 - - - -
374A ILE* 4.4 14.6 - - + -
377A TRP* 5.0 5.4 - - + -
378A LEU* 5.8 1.1 - - + -
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Residues in contact with LEU 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 GLU* 2.8 36.0 + - + +
311A THR* 4.0 5.8 - - - +
313A LEU* 1.3 72.1 - - - +
315A PHE* 1.3 60.5 + - - +
317A THR* 3.0 15.8 + - - +
318A SER* 2.8 21.9 + - - -
352A TYR* 3.7 24.9 - - + +
356A VAL* 6.0 1.1 - - + -
357A VAL* 4.1 24.9 - - + -
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Residues in contact with PHE 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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311A THR 3.0 20.3 + - - +
312A LYS* 3.6 4.3 - - - +
313A LEU 3.2 0.2 - - - -
314A LEU* 1.3 76.8 - - - +
316A MSE 1.3 59.0 + - - +
318A SER* 3.9 4.3 - - - -
319A ARG* 2.8 65.0 + - + +
320A VAL* 3.6 21.4 + - + -
328A TYR* 3.8 15.7 - + - -
98B PHE* 4.1 11.7 - + - -
99B CYS* 3.5 43.1 - - + -
100B MET* 3.3 26.0 - - - -
101B VAL* 4.0 7.4 - - + -
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Residues in contact with MSE 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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312A LYS 3.0 20.9 + - - +
313A LEU* 3.3 20.4 + - - +
315A PHE* 1.3 76.3 - - - +
317A THR* 1.3 60.6 + - - +
318A SER 3.5 0.7 + - - -
320A VAL* 3.6 20.8 + - + +
325A GLN 5.0 0.4 - - - +
328A TYR* 4.3 14.1 - - + +
329A GLN* 3.7 31.6 - - + +
332A PHE* 4.8 6.1 - - - -
369A LEU* 3.5 43.0 - - + +
374A ILE* 4.1 14.1 - - + -
377A TRP* 4.0 18.2 - - + -
98B PHE* 3.9 28.9 - - + -
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU 2.9 20.5 + - - +
314A LEU* 3.0 14.0 + - - +
316A MSE 1.3 74.4 - - - +
318A SER* 1.3 59.2 + - - +
353A ILE* 4.5 12.8 - - + -
357A VAL* 3.8 29.6 - - + +
359A PRO* 4.8 7.0 - - - +
363A VAL* 3.9 11.8 - - - +
368A ILE* 3.6 12.1 - - - +
369A LEU 4.1 10.1 - - - +
371A ARG* 4.7 12.1 - - + -
374A ILE* 3.5 24.7 - - + -
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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