Contacts of the helix formed by residues 306 - 313 (chain B) in PDB entry 2A1A
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 GLU 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B TYR* 2.8 40.2 + - + +
303B GLU* 3.3 31.5 - - - +
304B LYS 2.9 0.6 - - - -
305B ALA* 1.3 78.2 - - - +
307B ARG* 1.3 65.5 + - - +
309B VAL* 3.0 15.3 + - + +
310B LYS* 2.9 56.0 + - + +
362B LEU* 4.4 2.7 - - + -
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Residues in contact with ARG 307 (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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303B GLU 4.2 2.0 + - - +
304B LYS* 3.0 50.8 + - - +
306B GLU* 1.3 77.6 - - - +
308B GLU* 1.3 65.7 + - - +
309B VAL 3.1 0.2 + - - -
310B LYS* 3.1 10.5 + - + +
311B ALA* 2.8 26.2 + - - +
413B ARG* 4.6 3.0 - - - +
434B GLY 6.6 0.2 - - - -
435B LEU* 5.7 2.6 - - - +
436B VAL* 3.6 28.7 + - + +
437B THR* 3.7 22.9 + - - +
446B TPO 2.7 44.1 + - - -
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LYS* 2.7 41.4 + - - -
298B VAL* 5.0 9.2 - - - +
304B LYS 4.4 0.2 + - - -
305B ALA* 3.9 13.3 + - - +
306B GLU 3.2 0.2 - - - -
307B ARG* 1.3 78.9 - - - +
309B VAL* 1.3 59.6 + - + +
311B ALA* 3.4 2.6 + - - +
312B LEU* 2.9 32.9 + - + +
362B LEU* 5.8 0.2 - - - +
364B ILE* 4.2 27.2 - - + +
366B MET* 4.9 1.9 - - - +
432B ASP* 4.4 1.2 - - - -
433B PHE* 3.4 39.9 + - + +
434B GLY* 3.4 16.3 - - - -
436B VAL* 3.6 3.0 - - - +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU* 3.0 25.4 + - + +
308B GLU* 1.3 74.4 - - + +
310B LYS* 1.3 65.0 + - + +
311B ALA 3.1 1.3 - - - -
312B LEU* 4.2 5.3 - - - +
313B ALA* 2.9 34.0 + - - +
323B TYR* 3.9 13.5 - - + +
326B CYS* 3.9 26.5 - - + -
362B LEU* 4.2 15.0 - - + -
364B ILE* 3.5 38.8 - - + -
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Residues in contact with LYS 310 (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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303B GLU* 5.2 5.5 + - - -
306B GLU* 2.9 53.0 + - + +
307B ARG* 3.7 9.9 - - + +
309B VAL* 1.3 81.3 - - + +
311B ALA* 1.3 60.3 + - - +
313B ALA* 3.9 5.6 - - - +
314B LYS* 3.4 32.6 + - - +
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Residues in contact with ALA 311 (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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307B ARG 2.8 19.2 + - - +
308B GLU 3.6 4.7 - - - +
310B LYS* 1.3 69.0 - - - +
312B LEU* 1.3 61.9 + - - +
313B ALA 3.1 0.9 - - - -
314B LYS* 2.8 24.3 + - - +
315B LEU* 3.0 21.5 + - + +
410B LEU* 3.6 26.7 - - + -
433B PHE* 4.8 1.8 - - + -
436B VAL* 3.6 21.3 - - + -
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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
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308B GLU* 2.9 27.7 + - + +
309B VAL* 4.2 1.1 - - - +
311B ALA* 1.3 72.8 - - - +
313B ALA* 1.3 63.1 + - - +
315B LEU* 3.0 23.7 + - + +
320B ILE* 4.3 9.6 - - + -
321B VAL* 4.2 16.2 - - + +
323B TYR* 3.6 30.8 - - + +
364B ILE* 3.5 31.4 - - + -
366B MET* 4.5 14.1 - - + -
431B GLY 6.4 0.2 - - - -
433B PHE* 3.4 41.7 - - + +
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Residues in contact with ALA 313 (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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309B VAL 2.9 19.7 + - - +
310B LYS* 3.9 6.7 - - - +
311B ALA 3.1 0.2 - - - -
312B LEU* 1.3 76.3 - - - +
314B LYS* 1.3 59.3 + - + +
315B LEU 5.1 0.2 - - - -
323B TYR* 3.7 26.3 - - + +
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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
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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