Contacts of the helix formed by residues 261 - 283 (chain P) in PDB entry 5D4D
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 PRO 261 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N TYR* 3.5 38.6 - - + +
259P ARG* 3.9 26.7 - - - +
260P ILE* 1.3 89.2 - - + +
262P VAL* 1.3 64.6 + - + +
263P HIS* 3.4 26.7 - - + +
264P MET* 3.0 16.3 + - + +
265P VAL 3.1 6.4 + - - -
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Residues in contact with VAL 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249P ARG* 5.0 15.9 - - + +
252P ALA* 4.2 23.6 - - + +
253P ASP* 5.1 9.6 - - - +
259P ARG* 5.0 5.9 - - - +
260P ILE 3.6 0.8 + - - +
261P PRO* 1.3 71.2 - - + +
263P HIS* 1.3 67.3 + - + +
265P VAL* 3.1 12.4 + - - +
266P GLU* 3.0 31.3 + - + +
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Residues in contact with HIS 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 5.6 1.2 + - - -
261P PRO* 3.9 22.8 - - + +
262P VAL* 1.3 82.6 - - + +
264P MET* 1.3 86.2 + - + +
266P GLU* 3.1 22.0 + - - +
267P THR* 2.9 31.0 + - - -
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Residues in contact with MET 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 3.7 25.6 - - + +
35N ARG* 3.3 29.6 - - - +
260P ILE* 3.4 16.2 - - + -
261P PRO* 3.0 13.1 + - + +
263P HIS* 1.3 93.4 - - + +
265P VAL* 1.3 58.1 + - - +
267P THR* 3.3 16.0 + - - -
268P ILE* 2.9 37.0 + - - +
307P THR* 5.5 6.1 - - - +
310P ILE* 5.0 16.8 - - + -
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Residues in contact with VAL 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252P ALA* 4.0 32.1 - - + +
256P ARG* 5.1 13.5 - - - +
260P ILE* 3.1 37.7 - - + +
261P PRO 3.1 6.9 + - - +
262P VAL* 3.2 11.7 - - - +
264P MET* 1.3 74.6 - - - +
266P GLU* 1.3 57.4 + - + +
268P ILE* 3.3 5.8 + - + +
269P ASN* 2.3 56.6 + - - +
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Residues in contact with GLU 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262P VAL* 3.0 19.1 + - - +
263P HIS* 3.1 22.4 + - - +
265P VAL* 1.3 76.0 - - + +
267P THR* 1.3 57.0 + - - +
269P ASN* 3.8 5.9 - - - +
270P LYS* 2.9 31.0 + - - +
273P ARG* 4.9 1.4 + - - -
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Residues in contact with THR 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263P HIS 2.9 15.4 + - - -
264P MET* 3.5 19.9 - - - +
266P GLU* 1.3 76.7 - - - +
268P ILE* 1.3 57.5 + - + +
270P LYS* 3.2 12.8 - - + +
271P LEU* 2.9 28.4 + - + +
295P MET* 5.8 0.8 - - - +
299P TRP* 4.0 33.1 - - + -
307P THR* 4.4 12.6 - - + -
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Residues in contact with ILE 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256P ARG* 4.3 12.6 - - - +
260P ILE* 3.8 31.4 - - + -
264P MET* 2.9 27.2 + - + +
265P VAL* 3.8 5.6 - - + +
267P THR* 1.3 72.8 - - - +
269P ASN* 1.3 66.6 + - - +
270P LYS 3.1 1.6 - - - -
271P LEU* 3.2 9.2 + - + +
272P SER* 2.8 33.2 + - - +
307P THR* 4.0 19.3 - - + -
308P LEU* 6.1 2.2 - - + -
310P ILE* 4.2 10.1 - - + -
311P ALA* 3.6 32.5 - - + -
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Residues in contact with ASN 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P VAL* 2.3 57.2 + - - +
266P GLU* 3.9 5.6 - - - +
268P ILE* 1.3 78.0 - - - +
270P LYS* 1.3 57.3 + - - +
272P SER* 3.4 8.9 + - - -
273P ARG* 2.9 39.2 + - + +
276P ARG* 4.6 0.7 + - - -
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Residues in contact with LYS 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P GLU 2.9 15.7 + - - +
267P THR* 3.2 15.5 - - + +
269P ASN* 1.3 75.5 - - - +
271P LEU* 1.3 67.1 + - - +
273P ARG* 3.1 30.7 + - - +
274P THR* 2.9 32.4 + - - +
295P MET* 4.4 30.1 + - + -
299P TRP* 5.9 2.0 - - - +
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Residues in contact with LEU 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267P THR* 2.9 15.7 + - + +
268P ILE* 3.4 10.8 - - + +
270P LYS* 1.3 75.0 - - - +
272P SER* 1.3 58.3 + - - +
274P THR* 3.4 2.1 + - - +
275P ALA* 2.9 32.6 + - - +
291P ILE* 4.5 14.3 - - + +
295P MET* 3.7 33.9 - - + -
299P TRP* 4.1 23.8 - - + -
304P VAL* 4.0 10.8 - - + +
307P THR* 3.6 27.6 - - + -
308P LEU* 3.8 33.9 - - + -
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Residues in contact with SER 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376M ARG* 5.4 1.0 + - - -
268P ILE* 2.8 21.9 + - - +
269P ASN* 3.5 11.0 - - - -
270P LYS 3.2 0.2 - - - -
271P LEU* 1.3 77.2 - - - +
273P ARG* 1.3 56.9 + - - +
275P ALA* 3.8 4.3 - - - +
276P ARG* 2.9 47.1 + - - +
308P LEU* 5.6 6.3 - - - +
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Residues in contact with ARG 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P GLU 4.9 1.4 + - - -
269P ASN* 2.9 19.3 + - + +
270P LYS* 3.1 41.0 + - - +
272P SER* 1.3 72.3 - - - +
274P THR* 1.3 70.7 + - - +
276P ARG* 3.1 27.1 + - - +
277P GLN* 2.9 26.9 + - - +
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Residues in contact with THR 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270P LYS* 2.9 23.0 + - - +
271P LEU* 3.6 4.3 - - - -
273P ARG* 1.3 78.6 + - - +
275P ALA* 1.3 59.1 + - - +
277P GLN* 3.0 10.4 + - - +
278P LEU* 2.9 31.8 + - + +
291P ILE* 4.7 6.5 - - + -
294P ALA* 3.9 31.9 + - + +
295P MET* 3.1 29.4 - - + +
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Residues in contact with ALA 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376M ARG* 4.5 5.0 + - - +
271P LEU 2.9 18.3 + - - +
272P SER* 4.0 3.6 - - - +
274P THR* 1.3 77.3 - - - +
276P ARG* 1.3 56.8 + - - +
278P LEU* 3.8 6.0 - - - +
279P GLN* 3.0 29.5 + - - +
286P PRO* 3.9 16.2 - - + +
291P ILE* 3.6 26.5 - - + -
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Residues in contact with ARG 276 (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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373M VAL 5.9 0.2 - - - -
374M ASN* 3.2 37.5 + - - +
375M SER* 5.9 1.1 - - - +
376M ARG* 3.4 50.2 - - - +
269P ASN 4.6 0.8 + - - -
272P SER* 2.9 29.7 + - - +
273P ARG* 3.2 43.6 + - - +
275P ALA* 1.3 77.1 - - - +
277P GLN* 1.3 57.6 + - - +
279P GLN* 3.8 3.6 - - - +
280P GLN* 2.9 33.5 + - + +
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Residues in contact with GLN 277 (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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370M ALA* 6.2 1.2 - - - +
371M LYS* 4.8 22.6 - - - +
273P ARG 2.9 13.5 + - - +
274P THR* 3.0 11.4 + - - +
276P ARG* 1.3 74.5 - - + +
278P LEU* 1.3 61.8 + - + +
279P GLN 3.1 0.9 - - - -
280P GLN* 2.8 38.8 + - - +
281P GLU* 3.0 34.2 + - - +
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Residues in contact with LEU 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274P THR* 2.9 20.3 + - + +
275P ALA* 3.8 0.4 - - - +
277P GLN* 1.3 75.0 - - - +
279P GLN* 1.3 57.9 + - - +
281P GLU* 3.4 16.4 - - - +
282P LEU* 2.9 52.7 + - + +
284P ARG 4.5 0.7 - - - -
286P PRO* 3.7 18.6 - - + -
290P GLU* 3.6 29.4 - - + +
291P ILE* 3.7 23.8 - - + +
294P ALA* 3.7 24.0 - - + -
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Residues in contact with GLN 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M PHE* 3.4 34.2 + - + +
116M GLY* 4.0 2.4 - - - +
375M SER* 4.4 4.2 + - - -
376M ARG* 2.7 45.8 + - - +
379M GLU* 3.2 19.8 + - - -
275P ALA 3.0 17.1 + - - +
276P ARG 3.8 3.4 - - - +
278P LEU* 1.3 75.7 - - - +
280P GLN* 1.3 65.2 + - - +
281P GLU 3.1 0.2 - - - -
283P GLY 3.0 20.8 + - - -
284P ARG 3.2 22.6 + - - +
285P GLU* 3.0 22.7 + - - +
286P PRO* 4.1 3.4 - - + +
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Residues in contact with GLN 280 (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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112M GLU 5.4 1.6 - - - +
113M VAL* 4.3 12.9 - - + +
114M PHE* 3.5 34.6 + - - +
370M ALA* 2.4 54.1 + - - +
371M LYS* 4.7 0.9 - - - +
373M VAL 4.3 9.3 + - - +
276P ARG* 2.9 20.2 + - + +
277P GLN* 2.8 40.1 + - + +
279P GLN* 1.3 77.3 - - - +
281P GLU* 1.3 57.8 + - - +
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Residues in contact with GLU 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M TYR* 5.4 4.2 + - - -
114M PHE* 5.3 0.7 - - - +
277P GLN* 3.0 29.6 + - - +
278P LEU* 3.4 22.6 - - - +
280P GLN* 1.3 77.2 - - - +
282P LEU* 1.3 69.7 + - + +
283P GLY* 2.9 12.4 + - - -
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Residues in contact with LEU 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M TYR* 5.0 1.5 + - - -
278P LEU* 2.9 46.5 + - + +
281P GLU* 1.3 77.9 - - + +
283P GLY* 1.3 61.2 + - - +
284P ARG* 3.2 46.5 + - + +
286P PRO* 4.8 1.8 - - + -
290P GLU* 3.1 24.9 - - - +
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Residues in contact with GLY 283 (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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93M PRO* 4.7 1.7 - - - +
95M TYR* 4.0 12.3 + - - -
114M PHE* 3.1 41.0 - - - -
117M HIS* 3.7 8.0 + - - -
279P GLN 3.0 11.0 + - - -
281P GLU 2.9 6.8 + - - -
282P LEU* 1.3 75.2 - - - +
284P ARG* 1.3 65.4 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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