Contacts of the helix formed by residues 317 - 327 (chain A) in PDB entry 2OG9
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 ALA 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A PHE* 4.2 23.8 - - + -
290A PRO* 4.4 9.4 - - + -
316A PHE* 1.3 104.1 - - + +
318A MSE 1.3 61.2 + - - +
319A GLU* 3.1 10.3 - - - -
320A LEU* 3.1 5.7 + - + -
321A HIS* 2.9 33.0 + - + +
337A PHE* 4.1 2.1 - - - -
340A LEU* 4.3 3.6 - - - -
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Residues in contact with MSE 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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316A PHE 3.1 7.5 + - - -
317A ALA* 1.3 72.9 - - - +
319A GLU* 1.3 85.5 + - - +
321A HIS* 4.2 2.0 - - - +
322A VAL* 2.9 29.1 + - - +
334A VAL* 4.0 15.5 - - + -
335A GLU 3.5 16.2 - - - +
336A HIS* 3.7 22.7 - - + +
337A PHE* 3.7 41.3 - - + +
341A GLU* 4.2 19.7 - - + +
348A ILE* 3.7 31.4 - - + +
355A MSE 3.8 12.8 - - + -
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 5.2 4.5 - - + -
317A ALA* 3.1 3.4 - - - -
318A MSE 1.3 104.8 + - + +
320A LEU* 1.3 57.0 + - - +
322A VAL* 3.9 1.7 - - - +
323A HIS* 3.5 21.8 + - - -
337A PHE* 4.9 3.2 - - - +
340A LEU* 3.8 27.7 - - - +
341A GLU* 4.2 11.6 + - - +
344A PHE* 4.1 18.0 - - + -
346A GLU 6.1 0.7 - - - +
348A ILE* 4.5 18.6 - - + +
358A PRO* 5.6 0.5 - - - +
363A LEU* 4.3 8.8 - - - +
365A LEU* 3.8 38.3 - - + +
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Residues in contact with LEU 320 (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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65A PHE* 4.8 12.6 - - + +
124A VAL* 4.3 20.4 - - + -
138A LEU* 4.0 3.6 - - + -
289A ALA* 3.6 26.9 - - + -
290A PRO* 3.9 18.8 - - + -
295A ILE* 3.8 25.4 - - + -
317A ALA* 3.1 12.1 + - + +
318A MSE 3.0 0.2 - - - -
319A GLU* 1.3 78.9 - - - +
321A HIS* 1.3 65.6 - - + +
322A VAL 3.3 1.8 - - - -
323A HIS* 3.2 15.6 + - - +
324A LEU* 3.4 17.2 + - + +
363A LEU* 3.5 26.7 - - + -
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Residues in contact with HIS 321 (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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287A PRO 4.1 2.0 - - - -
288A ASP* 3.9 6.2 + - - -
289A ALA* 3.0 45.3 + - + -
290A PRO* 4.0 5.4 - - + +
298A PHE* 3.8 9.9 - + - -
314A PRO* 3.5 23.9 - - + +
315A HIS 3.1 19.5 + - - -
316A PHE 2.7 31.1 - - - +
317A ALA* 2.9 16.8 + - + +
318A MSE 4.4 2.9 - - - -
320A LEU* 1.3 74.6 - - + +
322A VAL* 1.3 57.5 + - - +
324A LEU* 3.8 14.1 - - - +
325A ALA* 2.7 37.1 + - - +
334A VAL* 4.6 7.9 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 4.1 5.5 - - + +
318A MSE 2.9 22.7 + - - +
319A GLU 3.9 4.5 - - - +
321A HIS* 1.3 76.3 - - - +
323A HIS* 1.3 74.9 + - + +
325A ALA* 4.0 5.3 - - - +
326A ALA* 3.2 22.3 + - - +
334A VAL* 4.6 7.1 - - - +
348A ILE* 4.3 7.9 - - + -
355A MSE 3.9 29.6 - - + -
356A LEU 4.0 5.8 - - - +
357A VAL* 3.8 30.1 - - + +
358A PRO* 3.7 21.3 - - + -
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Residues in contact with HIS 323 (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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137A SER* 4.0 5.8 - - - -
138A LEU* 3.8 20.2 - - + -
139A ALA* 3.2 37.5 + - - +
142A LEU* 4.6 1.8 - - - +
319A GLU 3.5 22.6 + - - -
320A LEU 3.2 7.8 + - - +
321A HIS 3.1 0.6 - - - -
322A VAL* 1.3 79.8 - - + +
324A LEU* 1.3 65.3 + - - +
326A ALA* 3.3 12.0 + - - +
327A ALA* 3.4 10.0 + - - +
357A VAL* 4.0 1.9 - - + +
358A PRO* 3.8 40.6 - - + +
360A ARG 5.1 0.2 - - - -
362A GLY 3.8 15.0 + - - -
363A LEU* 3.3 31.3 + - + -
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Residues in contact with LEU 324 (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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138A LEU* 4.6 4.7 - - + -
142A LEU* 3.7 25.8 - - + -
289A ALA* 3.9 16.2 - - + -
295A ILE* 4.0 25.1 - - + -
298A PHE* 3.7 41.7 - - + -
299A LEU* 4.4 4.9 - - + -
312A LEU* 5.0 2.1 - - - +
320A LEU* 3.4 20.8 + - + +
321A HIS* 3.2 27.3 + - + +
323A HIS* 1.3 75.6 - - - +
325A ALA* 1.3 62.3 + - - +
327A ALA* 3.1 17.0 + - - +
328A TYR* 3.6 7.1 + - - +
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Residues in contact with ALA 325 (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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146A ARG* 3.0 16.6 + - - -
149A VAL* 4.2 4.3 - - + -
312A LEU* 4.7 5.4 - - - -
314A PRO* 4.5 7.5 - - + +
321A HIS 2.7 21.5 + - - +
322A VAL 4.0 3.4 - - - +
324A LEU* 1.3 73.1 - - - +
326A ALA* 1.3 62.8 + - - +
328A TYR* 3.1 10.8 + - - +
332A PRO* 3.3 28.3 - - + +
334A VAL* 3.5 25.4 - - + -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA* 4.0 13.2 - - + -
144A SER* 4.1 2.7 - - - -
145A TYR 2.8 26.6 + - - -
146A ARG* 3.4 29.5 + - - +
149A VAL* 4.1 1.8 - - - +
322A VAL 3.2 19.5 + - - +
323A HIS 3.5 7.2 - - - +
324A LEU 3.2 0.2 - - - -
325A ALA* 1.3 77.5 - - - +
327A ALA* 1.3 57.9 + - - +
357A VAL* 3.7 21.8 - - + -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA 4.9 1.1 - - - +
142A LEU* 4.1 24.5 - - + +
143A GLY 3.4 24.4 - - - +
144A SER* 4.2 0.2 - - - +
145A TYR* 3.5 15.4 - - - -
299A LEU* 6.0 2.7 - - + -
323A HIS 3.4 8.0 + - - +
324A LEU* 3.1 11.1 + - - +
325A ALA 3.1 1.2 - - - -
326A ALA* 1.3 79.3 - - - +
328A TYR* 1.3 60.2 + - - +
329A PRO* 3.8 2.3 - - - +
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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
------------------------------------------------------------
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