Contacts of the helix formed by residues 296 - 318 (chain B) in PDB entry 2R5N
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 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B HIS* 3.8 29.4 - - + +
49B PRO* 3.5 11.8 - - + +
78B THR* 2.8 20.1 + - + +
294B TRP 3.4 2.2 + - - +
295B ASP* 1.3 73.9 - - - +
297B LYS* 1.3 59.9 + - - +
298B GLU 3.4 2.5 - - - -
299B ALA* 4.2 9.0 - - + +
300B GLY* 2.8 31.4 + - - +
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Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 4.1 2.2 - - - +
49B PRO* 4.4 12.1 - - + -
50B GLN* 4.0 28.1 - - + +
78B THR 4.4 2.7 - - - +
79B GLY* 3.4 29.3 - - - +
295B ASP* 2.6 40.7 + - - +
296B ALA* 1.3 77.9 - - - +
298B GLU* 1.3 60.8 + - + +
301B GLN* 2.9 32.1 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP* 4.4 4.5 + - - +
296B ALA 3.4 0.4 - - - -
297B LYS* 1.3 76.8 - - + +
299B ALA* 1.3 65.0 + - - +
301B GLN* 3.9 3.5 - - - +
302B ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ALA* 3.7 12.3 + - + +
298B GLU* 1.3 77.4 - - - +
300B GLY* 1.3 58.0 + - - +
302B ALA* 3.2 7.4 + - - +
303B LYS* 2.9 54.1 + - - +
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Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B HIS 3.2 26.0 - - - +
48B ASN* 3.5 20.7 - - - +
54B TRP* 4.8 0.3 - - - -
296B ALA* 2.8 23.0 + - - +
297B LYS 3.8 0.7 - - - -
299B ALA* 1.3 73.3 - - - +
301B GLN* 1.3 56.5 + - - +
303B LYS* 3.3 4.3 + - - +
304B GLU* 2.9 25.5 + - - +
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 2.9 26.8 + - - +
50B GLN* 3.5 25.6 - - - +
51B ASN* 5.7 0.3 - - - +
297B LYS 2.9 18.2 + - - +
298B GLU* 4.1 3.6 - - - +
300B GLY* 1.3 75.3 - - - +
302B ALA* 1.3 57.7 + - - +
304B GLU* 4.5 7.5 - - - +
305B SER* 2.8 61.8 + - - +
308B ASN* 5.1 4.2 - - - +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU 3.1 14.5 + - - +
299B ALA* 3.2 10.9 + - - +
301B GLN* 1.3 75.5 - - - +
303B LYS* 1.3 58.3 + - + +
305B SER* 3.9 4.5 - - - -
306B ALA* 3.0 30.7 + - - +
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Residues in contact with LYS 303 (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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44B PHE 5.3 2.6 + - - -
45B LEU 3.9 18.8 + - - -
46B LYS* 4.1 24.9 - - + +
47B HIS* 4.8 4.1 + - - +
54B TRP* 3.9 16.4 - - + -
299B ALA* 2.9 36.6 + - - +
300B GLY* 3.8 7.2 - - - +
302B ALA* 1.3 77.7 - - + +
304B GLU* 1.3 61.9 + - - +
306B ALA* 3.4 7.4 + - - +
307B TRP* 3.0 22.3 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 2.8 36.1 + - - +
51B ASN* 2.8 37.7 + - - +
54B TRP* 3.5 41.9 - - + +
300B GLY 2.9 16.5 + - - +
301B GLN* 4.1 7.0 - - - +
303B LYS* 1.3 76.4 - - - +
305B SER* 1.3 57.6 + - - +
307B TRP* 3.1 2.8 + - - +
308B ASN* 2.8 43.9 + - - +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B GLN* 2.8 39.0 + - - +
302B ALA* 3.9 4.5 - - - -
304B GLU* 1.3 76.0 - - - +
306B ALA* 1.3 64.1 + - - +
308B ASN* 3.1 13.4 + - - +
309B GLU* 3.0 38.0 + - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 3.0 18.1 + - - +
303B LYS* 3.6 7.4 - - - +
305B SER* 1.3 75.1 - - - +
307B TRP* 1.3 63.8 + - - +
309B GLU* 3.3 13.8 + - - +
310B LYS* 3.0 21.9 + - - +
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Residues in contact with TRP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B TRP* 3.4 39.7 - + + +
55B ALA* 4.2 11.2 - - + -
56B ASP* 3.4 28.6 - - + +
144B ILE* 2.8 32.8 + - + +
303B LYS 3.0 7.7 + - - +
304B GLU 3.4 6.7 - - - +
306B ALA* 1.3 77.5 - - - +
308B ASN* 1.3 77.8 + - - +
310B LYS* 3.0 26.8 + - - +
311B PHE* 2.8 64.7 + + + -
325B PHE* 4.0 25.6 - + - -
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Residues in contact with ASN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B GLN* 5.1 4.2 - - - +
304B GLU* 2.8 38.4 + - - +
305B SER* 3.1 16.0 + - - +
307B TRP* 1.3 93.9 - - - +
309B GLU* 1.3 58.2 + - + +
311B PHE* 3.3 5.1 + - - +
312B ALA* 2.9 29.1 + - - +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B SER* 3.0 29.0 + - - +
306B ALA* 3.6 11.0 - - - +
308B ASN* 1.3 74.3 - - + +
310B LYS* 1.3 64.9 - - - +
312B ALA* 3.3 8.5 + - - +
313B ALA* 3.1 22.3 + - - +
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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
----------------------------------------------------------
56B ASP* 4.9 3.2 + - - -
141B GLY 5.9 1.3 - - - +
142B HIS* 4.7 6.9 + - - +
143B ASP* 3.3 36.2 + - + +
144B ILE* 4.3 10.5 - - + +
146B ASP* 5.4 4.8 + - - +
306B ALA 3.0 12.5 + - - +
307B TRP* 3.3 31.7 - - - +
309B GLU* 1.3 77.3 - - - +
311B PHE* 1.3 57.1 + - - +
313B ALA* 3.3 7.5 + - - +
314B TYR* 3.0 26.2 + - - +
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ILE* 4.0 19.0 - - + +
307B TRP* 2.8 50.5 + + + +
308B ASN* 3.7 5.2 - - - +
310B LYS* 1.3 70.5 - - - +
312B ALA* 1.3 60.9 + - - +
314B TYR* 3.2 21.5 + + - +
315B ALA* 2.8 30.8 + - + +
322B ALA* 3.6 25.1 - - + -
325B PHE* 3.5 23.8 - + + -
326B THR* 3.5 25.6 - - - -
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ASN 2.9 16.5 + - - +
309B GLU* 3.3 9.4 + - - +
311B PHE* 1.3 78.7 - - - +
313B ALA* 1.3 61.4 + - - +
315B ALA* 3.2 8.7 + - - +
316B LYS* 3.0 26.7 + - - +
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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
----------------------------------------------------------
142B HIS* 3.7 19.2 - - + +
309B GLU 3.1 12.5 + - - +
310B LYS* 3.6 9.4 - - - +
312B ALA* 1.3 76.1 - - - +
314B TYR* 1.3 63.3 + - - +
316B LYS* 3.3 10.8 + - - +
317B ALA* 3.2 17.0 + - - +
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Residues in contact with TYR 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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137B PHE* 2.7 39.3 + + - -
139B ARG* 4.0 7.4 - - + +
142B HIS* 3.5 32.4 + - + +
144B ILE* 3.5 40.4 - - + -
310B LYS 3.0 13.7 + - - +
311B PHE* 3.2 13.0 + + - +
313B ALA* 1.3 76.8 - - - +
315B ALA* 1.3 53.4 + - - +
317B ALA* 3.1 2.1 + - - +
318B TYR* 2.7 53.4 + + + +
321B GLU* 3.3 25.5 - - + +
322B ALA* 3.8 30.5 - - + -
325B PHE* 5.1 0.2 - - + -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PHE* 2.8 25.9 + - + +
312B ALA* 3.2 8.9 + - - +
314B TYR* 1.3 72.8 - - - +
316B LYS* 1.3 61.4 + - - +
318B TYR 4.2 0.4 - - - -
319B PRO* 3.1 27.8 - - + +
322B ALA* 3.5 26.9 - - + -
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA 3.0 15.0 + - - +
313B ALA* 3.4 13.2 - - - +
314B TYR 3.2 0.2 - - - -
315B ALA* 1.3 78.7 - - - +
317B ALA* 1.3 58.9 + - - +
319B PRO* 3.8 7.6 - - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 3.9 13.7 - - + +
313B ALA 3.2 10.7 + - - +
314B TYR 3.1 2.0 + - - +
316B LYS* 1.3 79.8 - - + +
318B TYR* 1.3 88.3 + - + +
319B PRO* 3.5 5.8 - - - +
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 3.5 45.7 - - + +
140B PRO* 4.3 9.9 + - - +
142B HIS* 3.8 17.0 - + - -
314B TYR* 2.7 35.5 + + + +
315B ALA 3.6 2.5 - - - -
317B ALA* 1.3 91.4 - - + +
319B PRO* 1.4 61.8 - - - +
321B GLU* 3.3 37.9 - - + +
322B ALA* 2.9 28.1 + - - +
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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
------------------------------------------------------------
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