Contacts of the helix formed by residues 305 - 314 (chain B) in PDB entry 2CSX
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 ASP 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO 5.0 2.4 - - - +
303B VAL 3.7 4.2 + - - +
304B VAL* 1.3 75.4 - - - +
306B PRO* 1.3 73.9 - - - +
307B TYR* 3.0 29.4 + - - +
308B GLU* 3.2 30.4 + - + +
309B VAL* 2.9 23.3 + - - +
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Residues in contact with PRO 306 (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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20B PRO 3.7 15.0 - - - +
21B HIS* 3.4 28.5 - - - +
22B LEU* 3.6 9.0 - - + +
25B ALA* 4.4 10.8 - - + -
83B LEU* 3.8 27.4 - - + -
86B PHE* 4.4 1.8 - - - -
87B LEU* 4.8 5.2 - - + -
304B VAL* 3.4 10.5 - - + +
305B ASP* 1.3 88.9 - - - +
307B TYR* 1.3 62.7 + - + +
309B VAL* 4.3 7.0 - - + -
310B VAL* 2.9 34.1 + - + +
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Residues in contact with TYR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU 5.3 1.8 - - - -
301A GLY* 4.2 25.8 - - - -
20B PRO* 5.9 3.8 - - + -
79B ARG 4.4 2.4 + - - -
82B LYS* 3.5 12.8 - - - +
83B LEU* 3.4 44.3 + - + +
86B PHE* 3.6 46.1 - + + -
305B ASP* 3.0 19.0 - - - +
306B PRO* 1.3 82.1 - - + +
308B GLU* 1.3 59.9 + - - +
310B VAL* 3.6 2.3 - - - +
311B GLN* 2.8 27.5 + - - +
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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
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298A LYS* 5.4 7.2 + - - +
305B ASP* 3.3 34.0 - - + +
307B TYR* 1.3 76.7 - - - +
309B VAL* 1.3 75.2 + - + +
311B GLN* 3.7 17.5 - - - +
312B GLU* 3.0 28.5 + - - +
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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
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22B LEU* 5.1 4.9 - - + -
304B VAL* 3.2 33.9 - - + -
305B ASP 2.9 14.3 + - - +
306B PRO* 4.0 5.4 - - + +
308B GLU* 1.3 83.4 - - + +
310B VAL* 1.3 62.1 + - + +
312B GLU* 4.8 2.7 - - - +
313B TYR* 3.3 33.5 + - + -
318B VAL* 3.8 21.8 - - + +
334B PHE* 3.6 33.9 - - + -
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Residues in contact with VAL 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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305A ASP* 4.3 2.4 - - - +
86B PHE* 3.7 17.3 - - + +
87B LEU* 3.9 22.2 - - + -
306B PRO* 2.9 25.4 + - + +
307B TYR 3.6 2.5 - - - +
309B VAL* 1.3 78.1 - - + +
311B GLN* 1.3 65.1 + - - +
312B GLU 3.1 1.6 - - - -
314B GLY* 2.9 21.5 + - - -
315B LEU* 3.4 38.1 - - + +
318B VAL* 4.1 23.6 - - + -
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Residues in contact with GLN 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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19A VAL* 3.7 39.2 + - + +
20A PRO 5.3 0.6 + - - -
21A HIS* 5.1 3.0 + - - +
298A LYS* 3.6 28.6 + - - +
303A VAL* 4.2 36.8 - - + +
305A ASP* 3.5 18.0 - - + +
306A PRO* 5.9 0.3 - - - +
86B PHE* 4.6 5.5 - - + -
307B TYR 2.8 18.5 + - - +
308B GLU* 3.2 14.9 + - - +
310B VAL* 1.3 72.4 - - - +
312B GLU* 1.3 64.0 + - - +
495B ARG* 3.3 11.3 + - - -
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Residues in contact with GLU 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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19A VAL* 4.4 22.3 - - + +
79A ARG* 3.1 19.0 + - - +
308B GLU* 3.0 17.4 + - - +
309B VAL* 3.9 4.9 - - - +
310B VAL 3.1 0.4 - - - -
311B GLN* 1.3 77.8 - - - +
313B TYR* 1.3 86.5 + - + +
336B LYS* 4.1 5.4 + - - -
495B ARG* 2.6 34.5 + - - +
497B GLY* 2.4 35.7 - - - +
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Residues in contact with TYR 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* 3.3 30.5 + - + +
312B GLU* 1.3 105.3 + - + +
314B GLY* 1.3 59.1 + - - +
317B GLU* 2.9 22.8 - - + +
318B VAL* 4.2 11.4 - - + -
334B PHE* 5.1 2.0 - + - -
336B LYS* 3.4 30.8 - - - +
339B ILE* 4.1 25.5 - - + +
340B LEU* 4.2 20.2 - - + -
343B ILE* 3.8 30.0 - - + +
495B ARG* 3.6 17.6 + - + +
497B GLY* 3.7 19.3 - - - -
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Residues in contact with GLY 314 (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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305A ASP* 4.5 2.7 - - - -
310B VAL* 2.9 20.7 + - - -
312B GLU 3.4 1.0 - - - -
313B TYR* 1.3 77.8 - - - +
315B LEU* 1.3 60.7 - - - -
317B GLU* 2.9 16.1 - - - +
318B VAL* 3.0 25.3 + - - +
495B ARG* 3.6 15.2 - - - +
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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