Contacts of the helix formed by residues 283 - 303 (chain F) in PDB entry 5YL4
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 283 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F ILE* 3.8 12.8 - - + -
267F PHE* 3.6 35.7 - - + -
271F LEU* 4.1 4.5 - - + -
279F LEU* 3.2 13.1 + - + +
281F ASN 3.3 0.6 - - - -
282F SER* 1.3 95.7 + - - +
284F LEU* 1.3 69.4 + - - +
285F LEU 3.3 1.8 - - - -
286F GLN* 3.1 18.2 + - - +
287F ILE* 3.2 33.1 + - + -
321F VAL* 3.7 33.2 - - + -
325F LEU* 4.3 6.5 - - + -
327F VAL* 3.5 13.8 - - + +
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Residues in contact with LEU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F SER* 5.1 2.0 - - - +
215F LEU* 4.8 12.3 - - + -
217F ARG* 5.7 1.1 - - - +
264F PHE* 3.8 36.3 - - + -
279F LEU* 2.8 29.0 + - + +
280F GLU* 3.6 40.4 + - - +
283F ILE* 1.3 72.4 - - - +
285F LEU* 1.3 57.3 + - - +
287F ILE* 3.1 25.0 + - + +
288F LYS* 2.8 45.7 + - + +
376F ILE* 5.3 9.2 - - + -
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Residues in contact with LEU 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F GLU* 3.1 21.5 + - + +
281F ASN* 4.2 22.4 - - + +
283F ILE 3.3 0.2 - - - -
284F LEU* 1.3 75.8 - - - +
286F GLN* 1.3 58.5 + - + +
288F LYS* 4.0 18.1 - - + +
289F HIS* 3.1 26.5 + - - +
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Residues in contact with GLN 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F ASN 5.1 1.4 + - - +
282F SER 2.9 29.6 + - - -
283F ILE 3.1 5.9 + - - +
285F LEU* 1.3 77.4 - - + +
287F ILE* 1.3 60.7 + - - +
289F HIS* 3.4 7.5 + - - +
290F ILE* 2.9 39.6 + - + +
325F LEU 3.1 14.1 + - - -
326F LYS* 3.6 14.6 - - - +
327F VAL* 3.2 36.5 + - + +
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Residues in contact with ILE 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F ILE* 4.5 12.8 - - + -
203F SER* 3.9 12.8 - - - +
215F LEU* 4.9 3.4 - - + -
264F PHE* 5.6 0.2 - - + -
283F ILE* 3.2 33.2 + - + +
284F LEU* 3.1 27.7 + - + +
286F GLN* 1.3 75.3 - - - +
288F LYS* 1.3 58.3 + - - +
290F ILE* 3.3 3.4 + - - +
291F ILE* 2.9 45.7 + - + +
319F PHE* 3.4 45.3 - - + -
327F VAL* 3.8 12.1 - - + -
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Residues in contact with LYS 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F LEU* 3.6 22.4 - - + -
280F GLU* 3.0 27.3 + - - -
284F LEU* 2.8 34.1 + - + +
285F LEU* 4.0 18.5 - - + +
287F ILE* 1.3 71.4 - - - +
289F HIS* 1.3 61.4 + - - +
291F ILE* 4.5 0.7 - - - -
292F ARG* 3.2 28.9 + - - +
376F ILE* 4.7 18.2 - - + +
378F LEU* 3.5 38.0 - - + +
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Residues in contact with HIS 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F TRP* 4.0 29.0 + + - -
285F LEU 3.1 18.5 + - - +
286F GLN* 3.6 8.7 - - - +
287F ILE 3.3 0.2 - - - -
288F LYS* 1.3 74.3 - - - +
290F ILE* 1.3 59.5 + - + +
292F ARG* 4.0 19.2 + - - +
293F SER* 2.7 55.6 + - - -
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Residues in contact with ILE 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F TRP* 3.6 61.2 - - + -
286F GLN* 2.9 29.0 + - + +
287F ILE 3.3 3.1 + - - +
289F HIS* 1.3 73.7 - - + +
291F ILE* 1.3 68.2 + - - +
293F SER* 3.3 4.4 + - - -
294F CYS* 2.9 26.4 + - - +
317F PHE* 5.3 0.9 - - + -
319F PHE* 3.8 30.7 - - + -
327F VAL* 4.1 18.6 - - + +
329F LEU* 4.1 17.5 - - + +
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Residues in contact with ILE 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F SER* 4.6 3.1 - - - -
205F VAL* 3.7 19.3 - - + -
213F ILE* 3.8 15.9 - - + -
215F LEU* 3.6 26.7 - - + -
287F ILE* 2.9 43.4 + - + +
290F ILE* 1.3 76.8 - - - +
292F ARG* 1.3 64.5 + - - +
294F CYS* 3.7 1.6 - - - +
295F LEU* 3.0 34.9 + - + +
317F PHE* 4.0 24.0 - - + -
319F PHE* 4.2 2.9 - - + -
378F LEU* 3.6 23.1 - - + -
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Residues in contact with ARG 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F ILE* 4.4 9.4 - - + -
288F LYS 3.2 16.3 + - - +
289F HIS* 4.1 20.0 + - - +
291F ILE* 1.3 82.5 - - - +
293F SER* 1.3 60.1 + - - +
296F MET* 3.0 56.1 + - + +
378F LEU* 3.7 41.5 - - + +
379F HIS* 4.0 6.7 - - - +
380F HIS* 3.5 44.1 + - - +
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Residues in contact with SER 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F GLU* 5.5 2.4 - - - +
87F LEU* 3.7 12.1 - - - +
93F TRP* 4.3 18.6 - - - -
289F HIS* 2.7 46.5 + - - -
290F ILE* 3.8 2.9 - - - -
292F ARG* 1.3 77.9 + - - +
294F CYS* 1.3 63.1 + - - +
296F MET* 4.6 2.2 - - - +
297F CYS* 3.3 23.7 + - - +
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Residues in contact with CYS 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 4.1 27.1 - - + +
77F LEU* 5.3 2.7 - - - -
80F LEU* 5.3 0.2 - - - +
81F ILE* 5.6 0.7 - - - -
87F LEU* 4.8 7.9 - - - -
93F TRP* 3.8 24.0 - - - -
290F ILE* 2.9 21.2 + - - +
291F ILE 3.7 3.4 - - - +
293F SER* 1.3 76.6 - - - +
295F LEU* 1.3 61.6 + - - +
297F CYS* 3.4 18.1 - - - +
298F ILE* 3.5 13.2 + - - +
317F PHE* 4.4 14.1 - - + -
329F LEU* 3.9 21.8 - - - -
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Residues in contact with LEU 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 3.9 22.9 - - + -
205F VAL* 3.8 7.2 - - + -
207F VAL* 3.6 24.0 - - + -
211F TYR* 2.7 37.0 + - + +
213F ILE* 3.6 34.3 - - + -
291F ILE* 3.0 26.2 + - + +
294F CYS* 1.3 72.4 - - - +
296F MET* 1.3 61.4 + - - +
297F CYS 3.2 0.4 - - - -
298F ILE* 3.4 8.9 + - + -
299F GLU 3.1 13.9 + - - -
302F ILE* 5.6 0.4 - - + -
315F PHE* 4.3 20.0 - - + -
317F PHE* 4.3 9.0 - - + -
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Residues in contact with MET 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F GLU* 5.7 0.2 - - - +
211F TYR* 4.2 12.8 - - - +
213F ILE* 3.7 25.4 - - + +
292F ARG* 3.0 39.2 + - + +
293F SER* 4.6 2.5 - - - +
295F LEU* 1.3 73.9 - - - +
297F CYS* 1.3 65.4 + - - +
299F GLU* 3.1 41.6 + - - +
300F PRO* 3.9 4.3 - - - +
378F LEU 4.8 9.4 - - - +
379F HIS* 6.0 1.6 - - - -
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Residues in contact with CYS 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LEU* 4.3 13.2 - - - -
84F SER* 3.4 34.8 - - - -
86F GLU* 3.8 28.0 - - + +
87F LEU* 4.0 17.3 - - + -
293F SER 3.3 15.9 + - - +
294F CYS 3.4 11.7 - - - +
296F MET* 1.3 80.5 - - - +
298F ILE* 1.3 60.5 + - - +
299F GLU 3.5 0.2 + - - -
300F PRO* 3.5 10.4 - - - +
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Residues in contact with ILE 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F GLY 5.2 1.6 - - - +
68F ALA* 4.7 9.9 - - + -
70F LYS* 5.5 5.8 - - + -
71F LEU* 4.1 31.2 - - + +
80F LEU* 3.7 37.9 - - + -
211F TYR* 3.6 6.5 - - - +
294F CYS 3.5 8.5 + - - +
295F LEU* 3.6 17.7 - - + +
297F CYS* 1.3 74.6 - - - +
299F GLU* 1.3 64.3 + - - +
300F PRO* 3.3 2.7 - - - -
301F ALA* 2.9 21.9 + - + +
302F ILE* 3.3 38.6 + - + +
315F PHE* 5.7 0.7 - - + -
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Residues in contact with GLU 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LEU 5.0 0.7 - - - +
211F TYR* 3.6 52.5 - - + +
295F LEU 3.1 10.4 + - - +
296F MET* 3.1 30.3 - - - +
297F CYS 3.3 0.6 - - - -
298F ILE* 1.3 74.8 - - - +
300F PRO* 1.3 66.5 - - + +
303F SER* 2.9 43.4 + - - -
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Residues in contact with PRO 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ARG* 2.9 27.0 + - - -
338A LYS 3.7 23.8 - - - +
339A ARG* 5.4 1.1 - - - -
340A SER* 4.2 7.6 + - - +
296F MET 3.9 4.7 - - - +
297F CYS 3.5 12.3 - - - +
298F ILE 3.5 3.8 - - - -
299F GLU* 1.3 94.6 - - + +
301F ALA* 1.3 55.9 - - - +
303F SER* 5.0 1.8 - - - -
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Residues in contact with ALA 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 3.4 13.7 + - + +
309A HIS* 3.1 26.3 + - + +
340A SER* 3.6 21.1 + - - +
67F GLY* 6.2 0.4 - - - -
298F ILE* 2.9 15.4 + - + +
300F PRO* 1.3 80.4 - - - +
302F ILE* 1.3 64.3 + - + +
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Residues in contact with ILE 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ARG* 3.6 4.5 + - - +
309A HIS* 5.4 0.3 - - - -
65F TYR* 3.2 37.5 - - + -
66F ARG* 3.2 26.7 + - - +
67F GLY* 3.6 23.6 - - - +
68F ALA* 4.5 4.7 - - + -
207F VAL* 6.1 0.2 - - + -
211F TYR* 3.5 33.0 - - + +
295F LEU* 5.6 0.4 - - + -
298F ILE* 3.6 34.8 - - + +
301F ALA* 1.3 86.9 - - + +
303F SER* 1.3 71.8 + - - +
304F THR* 3.3 6.6 + - - +
315F PHE* 5.4 4.0 - - + -
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Residues in contact with SER 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 2.8 34.0 + - - +
65F TYR* 4.0 7.2 - - - -
211F TYR* 4.4 10.0 - - - +
299F GLU* 2.9 35.7 + - - +
300F PRO* 5.0 1.6 - - - -
302F ILE* 1.3 76.5 - - - +
304F THR* 1.3 60.9 + - - +
305F LYS* 3.2 26.4 + - - +
307F LEU* 4.7 0.3 - - - +
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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