Contacts of the helix formed by residues 308 - 322 (chain B) in PDB entry 4O9U
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 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B MET* 2.9 25.2 + - + +
306B SER* 4.1 0.4 - - - +
307B GLN* 1.3 75.3 - - - +
309B GLN* 1.3 53.5 + - - +
310B HIS 2.6 17.5 + - - -
311B LYS* 2.7 19.4 + - - +
312B LEU* 3.3 6.4 + - - -
374B ILE* 4.8 0.2 - - + -
436B ALA* 4.0 9.0 - - + -
437B GLN* 3.4 35.7 - - + +
440B LEU* 3.9 12.1 - - + -
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 3.9 30.5 - - - +
307B GLN* 2.9 47.4 + - - +
308B ALA* 1.3 75.6 + - - +
310B HIS* 1.3 88.0 + - + +
311B LYS 3.4 0.2 - - - -
312B LEU* 3.6 9.5 + - - +
313B LYS* 3.2 29.3 + - - +
344B LEU* 3.2 46.7 - - + +
345B LEU* 4.8 5.1 - - + +
347B GLU* 4.6 6.8 + - - +
348B ALA* 3.6 4.8 - - + +
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Residues in contact with HIS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLN 4.6 3.1 - - - +
308B ALA 2.6 7.0 + - - -
309B GLN* 1.3 101.2 + - + +
311B LYS* 1.3 63.2 + - + +
312B LEU 3.3 0.2 - - - -
313B LYS* 4.2 1.6 - - - +
314B GLU* 3.3 27.0 + - - +
347B GLU* 3.4 28.4 + - + -
348B ALA* 3.7 29.9 - - + -
437B GLN* 5.5 1.6 - - - +
294D LYS* 5.1 17.3 - - + +
363D PRO 5.3 1.9 - - - +
364D GLU* 6.2 2.7 - - + -
367D THR* 3.6 39.7 - - + +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA 2.7 12.6 + - - +
310B HIS* 1.3 76.3 - - + +
312B LEU* 1.3 60.0 + - - +
314B GLU* 3.7 21.9 + - - +
315B LEU* 3.5 7.3 + - - +
437B GLN* 3.5 42.8 - - + +
440B LEU* 3.8 22.0 - - + +
441B THR* 3.4 31.6 + - + +
444B ILE* 3.0 26.7 - - + +
294D LYS* 4.9 5.2 - - - +
327D LYS* 3.8 9.1 - - - +
360D GLU 4.8 4.0 + - - -
364D GLU* 2.8 40.8 + - - +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PHE* 3.7 33.7 - - + -
299B PRO* 4.9 5.4 - - + -
303B MET* 4.7 15.7 - - + -
308B ALA* 3.3 7.2 + - + +
309B GLN* 3.7 8.3 - - - +
310B HIS 3.3 0.2 - - - -
311B LYS* 1.3 74.9 - - - +
313B LYS* 1.3 60.8 + - - +
314B GLU 3.2 1.1 - - - -
315B LEU* 3.0 6.2 + - - +
316B ALA* 2.9 25.8 + - - +
328B PHE* 4.0 25.1 - - + -
345B LEU* 4.3 17.3 - - + -
372B VAL* 5.9 0.2 - - + -
374B ILE* 4.4 18.8 - - + -
440B LEU* 3.8 32.5 - - + +
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Residues in contact with LYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLN 3.2 15.1 + - - +
310B HIS* 4.5 2.9 - - - +
312B LEU* 1.3 79.4 - - - +
314B GLU* 1.3 57.1 + - - +
316B ALA* 3.4 9.1 + - + +
317B ASP* 2.8 71.8 + - - +
328B PHE* 5.3 2.2 - - + -
345B LEU* 5.8 0.7 - - + -
348B ALA* 3.9 22.4 + - + +
349B GLY 3.6 25.6 + - - -
350B VAL* 3.4 32.1 - - + +
351B ASP 5.5 0.2 - - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS 3.3 16.9 + - - +
311B LYS* 3.7 30.3 + - - +
313B LYS* 1.3 80.7 - - - +
315B LEU* 1.3 59.7 + - - +
317B ASP* 3.8 7.8 + - - +
318B LEU* 3.4 19.8 + - - +
441B THR* 6.1 0.5 - - - +
444B ILE* 3.4 33.6 - - + +
448B LYS* 4.5 2.9 + - - +
360D GLU* 5.0 6.0 - - - +
363D PRO* 3.5 46.7 - - + +
364D GLU* 5.2 2.9 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 5.2 8.5 - - + -
297B PHE* 4.6 16.8 - - + -
311B LYS 3.5 4.6 + - - +
312B LEU* 3.0 10.1 + - - +
314B GLU* 1.3 80.7 - - - +
316B ALA* 1.3 63.9 + - - +
318B LEU* 3.2 11.3 + - + +
319B LEU* 3.1 28.8 + - + +
440B LEU* 3.7 26.5 - - + -
443B LEU* 3.9 23.3 - - + +
444B ILE* 3.6 33.0 - - + +
447B LEU* 3.8 28.5 - - + -
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PHE* 4.0 10.3 - - + -
312B LEU 2.9 12.6 + - - +
313B LYS* 3.4 10.3 + - + +
315B LEU* 1.3 77.2 - - - +
317B ASP* 1.3 58.4 + - - +
319B LEU* 3.2 14.2 + - - +
320B GLU* 2.9 28.3 + - - +
326B VAL* 3.8 12.0 - - + +
328B PHE* 3.9 27.6 - - + -
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LYS* 2.8 56.6 + - - +
314B GLU* 4.0 7.5 - - - +
316B ALA* 1.3 72.0 - - - +
318B LEU* 1.3 64.5 + - - +
319B LEU 3.1 1.8 - - - -
320B GLU* 3.4 21.1 + - - +
321B ALA* 3.2 25.1 + - - +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU 3.4 12.0 + - - +
315B LEU* 3.2 19.0 + - + +
317B ASP* 1.3 78.8 - - - +
319B LEU* 1.3 59.1 + - - +
321B ALA* 4.1 6.8 - - + +
322B ARG* 3.8 25.0 + - + +
444B ILE* 3.8 24.9 - - + -
447B LEU* 3.7 36.3 - - + +
448B LYS* 3.7 34.5 - - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 3.5 33.7 - - + +
295B VAL* 5.0 11.7 - - + -
297B PHE* 3.7 33.9 - - + -
315B LEU* 3.1 21.2 + - + +
316B ALA* 3.4 7.2 - - - +
317B ASP 3.1 0.6 - - - -
318B LEU* 1.3 77.6 - - - +
320B GLU* 1.3 61.5 + - - +
321B ALA 3.1 2.0 - - - -
322B ARG* 3.2 9.5 + - - -
323B GLY 3.3 0.2 + - - -
324B VAL* 2.9 43.5 + - + +
326B VAL* 3.6 15.0 - - + -
447B LEU* 3.8 24.0 - - + -
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ALA 2.9 17.1 + - - +
317B ASP* 3.4 22.6 + - - +
319B LEU* 1.3 74.8 - - - +
321B ALA* 1.3 60.1 + - - +
323B GLY* 3.2 13.2 + - - -
324B VAL 3.8 10.3 + - - +
326B VAL* 4.4 16.6 - - + +
354B LYS* 3.3 34.3 + - - -
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ASP 3.2 15.7 + - - +
318B LEU* 4.1 9.0 - - + +
319B LEU 3.1 0.4 - - - -
320B GLU* 1.3 73.8 - - - +
322B ARG* 1.3 58.0 + - + +
323B GLY* 2.8 11.9 + - - -
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Residues in contact with ARG 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 6.1 3.0 - - - +
290B ALA* 3.7 25.5 + - - +
291B TYR* 5.3 7.9 + - - -
318B LEU* 3.8 15.4 + - + +
319B LEU* 3.2 11.7 + - - +
321B ALA* 1.3 76.2 - - + +
323B GLY* 1.3 55.9 + - - +
324B VAL* 3.2 21.1 + - + +
447B LEU* 3.7 29.5 + - - +
450B LEU 3.1 33.9 + - - -
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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