Contacts of the helix formed by residues 317 - 334 (chain P) in PDB entry 5IYB
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 VAL 317 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258P MET* 3.9 10.5 - - + -
315P ALA* 4.0 5.7 - - - +
316P LYS* 1.3 88.4 - - + +
318P ARG* 1.3 65.6 + - - +
319P ALA* 4.1 10.3 - - + +
320P GLU* 3.1 48.0 + - + +
321P ILE 3.8 1.9 + - - -
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Residues in contact with ARG 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P LEU* 3.7 39.3 - - + +
225P LYS 5.2 0.4 + - - -
226P SER* 3.9 17.2 - - - +
227P GLU* 2.7 39.6 + - - -
258P MET* 3.9 11.0 - - + -
317P VAL* 1.3 72.7 - - - +
319P ALA* 1.3 63.8 + - - +
321P ILE* 2.9 22.4 + - - +
322P TYR* 3.0 37.3 + - + -
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Residues in contact with ALA 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317P VAL* 3.2 12.1 + - + +
318P ARG* 1.3 77.3 - - - +
320P GLU* 1.3 59.2 + - + +
322P TYR* 3.2 11.2 + - - +
323P GLU* 2.8 46.1 + - + +
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Residues in contact with GLU 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298P PRO* 3.4 39.1 - - + +
300P ILE* 4.3 8.5 - - + -
314P GLY 5.7 0.4 - - - -
315P ALA* 3.4 4.5 - - + -
316P LYS* 2.6 39.3 + - - +
317P VAL* 3.1 26.2 + - + +
319P ALA* 1.3 77.9 - - + +
321P ILE* 1.3 56.8 + - - +
323P GLU* 4.3 6.1 - - - +
324P ALA* 2.8 33.1 + - - +
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Residues in contact with ILE 321 (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 PRO* 4.5 19.1 - - + -
164P GLN 6.5 0.4 - - - -
165P LEU* 5.7 9.9 - - + -
258P MET* 4.7 5.8 - - + +
259P VAL 5.7 0.4 - - - -
260P GLY* 4.6 16.2 - - - +
261P SER 5.8 0.4 - - - +
300P ILE* 4.8 4.9 - - + -
312P LEU* 3.7 50.5 - - + +
315P ALA* 3.7 27.8 - - + -
317P VAL 4.5 2.0 - - - +
318P ARG* 2.9 15.7 + - - +
320P GLU* 1.3 75.2 - - - +
322P TYR* 1.3 64.6 + - + +
324P ALA* 3.8 3.1 - - - +
325P PHE* 2.9 32.6 + - + +
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Residues in contact with TYR 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P VAL* 5.4 0.7 - - - -
163P PRO* 3.4 55.0 + - + -
165P LEU* 4.0 15.7 - - + +
318P ARG* 3.0 51.6 + - + -
319P ALA* 3.2 9.5 + - - +
321P ILE* 1.3 77.6 - - + +
323P GLU* 1.3 53.7 + - + +
325P PHE* 3.4 6.5 + - - +
326P GLU* 2.6 44.8 + - - +
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Residues in contact with GLU 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297P LYS* 6.0 1.6 - - + +
298P PRO* 4.7 13.2 - - + +
319P ALA* 2.8 33.1 + - + +
320P GLU* 3.9 9.3 - - - +
322P TYR* 1.3 70.7 - - + +
324P ALA* 1.3 60.3 + - - +
326P GLU* 3.1 11.4 + - - +
327P ASN* 2.9 38.5 + - - +
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Residues in contact with ALA 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295P MET* 4.1 14.2 - - + +
298P PRO* 4.0 16.3 - - + +
300P ILE* 4.1 18.8 - - + -
302P LEU* 4.8 3.1 - - + +
312P LEU* 4.2 13.0 - - + -
320P GLU 2.8 22.8 + - - +
321P ILE 3.9 2.9 - - - +
323P GLU* 1.3 73.2 - - - +
325P PHE* 1.3 60.4 + - - +
327P ASN* 3.6 9.2 - - - +
328P ILE* 3.2 22.9 + - - +
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Residues in contact with PHE 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160P GLY* 4.4 12.1 - - - -
161P ILE* 3.9 28.5 - - + -
163P PRO* 4.0 21.5 - - + -
262P CYS* 3.4 26.9 - - - -
264P VAL* 4.8 9.2 - - + -
310P VAL* 5.4 8.1 - - + -
312P LEU* 4.5 11.1 - - + +
321P ILE* 2.9 20.4 + - + +
322P TYR* 3.7 4.9 - - - +
324P ALA* 1.3 73.6 - - - +
326P GLU* 1.3 65.1 + - - +
327P ASN 3.2 0.4 - - - -
328P ILE* 3.8 14.6 - - + -
329P TYR* 2.8 72.4 + + + +
332P LEU* 5.5 2.9 - - + -
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Residues in contact with GLU 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155P ALA* 4.3 23.6 - - + +
156P SER* 4.9 12.9 - - - +
322P TYR* 2.6 29.9 + - - +
323P GLU* 3.5 12.2 - - - +
325P PHE* 1.3 77.3 - - - +
327P ASN* 1.3 61.5 + - - +
329P TYR* 4.9 2.0 - - - -
330P PRO* 3.3 17.8 - - - +
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Residues in contact with ASN 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295P MET* 4.2 17.4 - - + +
297P LYS* 4.3 22.0 - - - +
323P GLU* 2.9 24.3 + - - +
324P ALA* 3.6 10.5 - - - +
326P GLU* 1.3 77.5 - - - +
328P ILE* 1.3 60.4 + - - +
330P PRO* 3.6 13.3 - - - +
331P ILE* 4.0 13.0 - - - +
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Residues in contact with ILE 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273P LEU* 5.5 5.8 - - + -
277P HIS* 5.9 0.2 - - + -
293P TYR* 4.1 37.5 - - + +
295P MET* 4.2 6.7 - - + -
302P LEU* 4.3 20.4 - - + -
304P ILE* 5.7 4.9 - - + -
310P VAL* 5.6 1.6 - - + -
324P ALA 3.2 12.9 + - - +
325P PHE* 3.1 24.4 + - + +
327P ASN* 1.3 78.8 - - - +
329P TYR* 1.3 64.5 + - - +
330P PRO* 3.5 0.9 - - - -
331P ILE* 3.3 23.9 + - + +
332P LEU* 3.0 52.7 + - + +
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Residues in contact with TYR 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156P SER* 4.6 7.9 - - - +
157P GLU* 6.3 0.4 - - + -
158P SER* 3.1 27.0 + - - -
159P SER 3.0 30.5 - - - -
160P GLY* 5.1 0.7 - - - -
161P ILE* 5.2 13.1 - - + +
264P VAL* 3.9 31.5 + - + +
266P PHE* 4.6 9.3 - + - -
325P PHE* 2.8 48.9 + + + +
326P GLU* 4.6 2.7 - - - +
328P ILE* 1.3 72.4 - - - +
330P PRO* 1.3 71.5 - - + +
332P LEU* 3.4 6.2 + - + -
333P LYS* 3.1 31.6 + - + +
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Residues in contact with PRO 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156P SER* 4.7 13.4 - - - -
157P GLU* 3.4 30.8 - - + +
326P GLU 3.3 21.1 - - - +
327P ASN* 3.6 10.5 - - - +
328P ILE 3.6 2.0 - - - -
329P TYR* 1.3 91.3 - - + +
331P ILE* 1.3 66.0 + - + +
333P LYS 3.3 0.5 + - - -
334P GLY* 3.0 20.4 + - - -
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Residues in contact with ILE 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273P LEU* 4.7 7.4 - - + -
277P HIS* 3.8 34.1 - - + +
293P TYR* 5.6 1.1 - - - +
327P ASN 4.0 17.7 - - - +
328P ILE* 3.3 21.9 + - + +
330P PRO* 1.3 78.3 - - + +
332P LEU* 1.3 64.1 + - + +
334P GLY* 3.1 13.7 + - - -
335P PHE* 3.4 39.7 + - + -
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Residues in contact with LEU 332 (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 VAL* 5.0 12.6 - - + -
266P PHE* 3.5 14.5 - - + -
268P ILE* 4.1 17.9 - - + +
273P LEU* 3.9 26.9 - - + -
304P ILE* 4.1 21.5 - - + -
310P VAL* 4.3 21.1 - - + -
325P PHE* 5.5 2.2 - - + -
328P ILE* 3.0 46.9 + - + +
329P TYR* 3.8 10.5 - - + +
331P ILE* 1.3 75.1 - - + +
333P LYS* 1.3 64.9 + - - +
335P PHE* 3.1 16.8 + - + +
336P ARG 3.5 6.6 + - - -
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Residues in contact with LYS 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157P GLU* 3.2 49.7 + - + +
158P SER* 4.2 20.5 - - - +
266P PHE* 3.5 25.7 - - + -
329P TYR* 3.1 21.5 + - + +
332P LEU* 1.3 76.1 - - - +
334P GLY* 1.3 56.4 + - - +
335P PHE 3.1 0.4 - - - -
336P ARG* 3.1 41.9 + - - +
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Residues in contact with GLY 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157P GLU* 4.5 1.9 + - - -
330P PRO 3.0 12.9 + - - -
331P ILE* 3.4 6.1 - - - -
332P LEU 3.1 0.6 - - - -
333P LYS* 1.3 77.0 - - - +
335P PHE* 1.3 71.8 + - - +
336P ARG 3.5 0.7 - - - -
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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