Contacts of the helix formed by residues 256 - 270 (chain P) in PDB entry 2D2I
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 ILE 256 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255P THR* 1.3 88.9 + - - +
257P THR* 1.3 65.8 + - - +
258P GLU* 4.0 26.5 - - + +
259P GLN* 2.8 31.7 + - + +
260P VAL* 3.2 9.9 + - - +
304P VAL* 3.6 9.9 - - - -
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Residues in contact with THR 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P ILE* 1.3 72.9 - - - +
258P GLU* 1.3 65.4 + - - +
260P VAL* 3.4 4.1 + - - +
261P ASN* 3.2 27.6 + - - +
299P SER 5.6 0.4 - - - +
302P THR* 3.5 29.3 + - + +
303P LEU* 3.8 6.4 - - - +
304P VAL* 3.1 37.9 + - - +
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Residues in contact with GLU 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P ILE* 3.2 21.4 - - + +
257P THR* 1.3 82.9 - - - +
259P GLN* 1.3 62.1 + - - +
261P ASN* 3.6 7.0 + - + +
262P GLU* 3.2 30.9 + - + +
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Residues in contact with GLN 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171P PHE* 4.1 15.3 - - + -
253P LYS* 5.7 3.1 + - - -
254P PRO 4.3 3.1 + - - +
255P THR* 2.5 49.5 + - - +
256P ILE* 2.8 24.8 + - + +
258P GLU* 1.3 72.4 + - - +
260P VAL* 1.3 64.0 + - - -
262P GLU* 3.0 25.2 + - - +
263P VAL* 3.1 17.3 + - + +
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Residues in contact with VAL 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P LEU* 5.2 4.3 - - + -
171P PHE* 3.9 22.2 - - + -
255P THR* 3.9 14.8 - - + +
256P ILE 3.2 14.6 + - - +
257P THR 4.0 1.1 - - - +
259P GLN* 1.3 74.6 - - - +
261P ASN* 1.3 65.0 + - - +
263P VAL* 3.2 6.0 - - + +
264P LEU* 3.0 39.4 + - + +
302P THR* 3.4 26.9 - - + -
304P VAL* 3.5 23.1 - - + -
310P VAL* 4.4 8.5 - - + -
312P VAL* 4.5 8.1 - - + -
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Residues in contact with ASN 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257P THR* 3.2 17.6 + - - +
258P GLU* 3.8 8.5 - - - +
259P GLN 3.1 0.6 - - - -
260P VAL* 1.3 81.1 - - - +
262P GLU* 1.3 57.6 + - - +
264P LEU* 3.6 10.9 + - - +
265P GLN* 2.9 30.2 + - - +
278P TYR* 3.4 27.1 + - - +
297P VAL* 4.4 1.2 - - - +
299P SER* 3.0 31.8 + - - +
302P THR* 2.7 33.4 + - - +
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Residues in contact with GLU 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258P GLU* 3.2 24.2 + - + +
259P GLN* 3.0 19.2 + - - +
261P ASN* 1.3 78.1 - - - +
263P VAL* 1.3 64.4 + - + +
265P GLN* 3.3 12.1 + - - +
266P LYS* 2.8 31.2 + - + +
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Residues in contact with VAL 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P VAL* 3.6 19.6 - - + +
167P LEU* 5.2 0.9 - - + -
170P ASN* 3.7 32.5 - - + +
171P PHE* 4.0 23.8 - - + -
259P GLN* 3.1 15.3 + - + +
260P VAL 3.2 13.0 - - - +
262P GLU* 1.3 79.6 - - + +
264P LEU* 1.3 64.7 + - + +
266P LYS* 3.5 7.0 - - - +
267P ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P VAL* 4.4 12.3 - - + +
166P VAL* 4.2 16.2 - - + -
167P LEU* 3.8 22.9 - - + -
260P VAL* 3.0 33.5 + - + +
261P ASN* 3.8 9.6 - - - +
263P VAL* 1.3 82.3 - - + +
265P GLN* 1.3 61.5 + - - +
267P ALA* 3.7 3.1 + - - +
268P SER* 3.2 22.3 + - - -
276P ILE* 4.3 12.8 - - + +
278P TYR* 4.3 4.2 - - + -
297P VAL* 4.0 41.1 - - + -
312P VAL* 4.1 18.8 - - + -
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Residues in contact with GLN 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261P ASN 2.9 18.7 + - - +
262P GLU* 3.7 9.8 + - - +
264P LEU* 1.3 75.9 - - - +
266P LYS* 1.3 68.3 + - - +
268P SER* 2.8 20.5 + - - +
269P GLN* 3.1 33.1 + - - +
278P TYR* 3.4 47.7 + - + -
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Residues in contact with LYS 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262P GLU* 2.8 23.9 + - + +
263P VAL* 3.5 9.0 - - - +
265P GLN* 1.3 72.0 - - - +
267P ALA* 1.3 63.8 + - - +
269P GLN* 2.9 25.8 + - - +
270P THR* 2.9 40.8 + - + +
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Residues in contact with ALA 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P VAL* 3.7 28.5 - - + -
263P VAL 2.9 17.3 + - - +
264P LEU* 3.8 5.6 - - - +
266P LYS* 1.3 76.6 - - - +
268P SER* 1.3 61.7 + - - +
270P THR* 3.0 9.3 + - - -
271P THR* 3.8 17.3 - - - +
272P MET* 2.6 31.9 + - + -
276P ILE* 4.7 2.2 - - + -
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Residues in contact with SER 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264P LEU 3.2 12.1 + - - -
265P GLN* 2.8 15.6 + - - +
267P ALA* 1.3 79.0 - - - +
269P GLN* 1.3 63.2 + - - +
272P MET* 4.2 4.0 - - - +
273P LYS* 3.2 23.7 - - - +
274P GLY 4.4 0.5 + - - -
276P ILE* 3.1 33.9 - - - +
277P LYS* 4.4 0.2 - - - -
278P TYR* 3.5 26.6 + - - +
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Residues in contact with GLN 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P GLN* 3.1 38.3 + - + +
266P LYS* 2.9 19.5 + - - +
268P SER* 1.3 85.9 - - - +
270P THR* 1.3 67.0 + - + +
273P LYS* 3.9 19.1 - - - +
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Residues in contact with THR 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266P LYS* 2.9 49.5 + - + +
267P ALA* 3.0 1.4 + - - -
269P GLN* 1.3 87.9 - - + +
271P THR* 1.3 85.7 + - - +
272P MET 3.2 1.1 - - - -
273P LYS* 3.1 17.9 + - - +
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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
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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