Contacts of the strand formed by residues 313 - 321 (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 GLN 313 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63F ASN 3.8 14.4 - - - +
64F TYR* 3.6 16.5 - - + -
65F TYR* 2.7 42.3 + - + +
68F ALA* 3.6 6.7 - - - +
72F CYS* 4.8 0.6 - - - -
205F VAL 3.6 1.0 - - - +
206F LEU* 3.6 7.1 - - - +
207F VAL 3.0 31.3 + - - +
312F PHE* 1.3 81.8 - - - +
314F LEU* 1.3 69.3 + - - +
315F PHE* 3.3 37.9 - - + -
334F GLY* 3.1 31.2 + - - +
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Residues in contact with LEU 314 (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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13F VAL* 3.9 32.3 - - + -
14F TYR* 3.8 20.6 + - + +
204F TRP* 4.2 14.8 - - + -
205F VAL 3.5 19.3 - - - +
206F LEU* 4.4 12.3 - - + +
313F GLN* 1.3 76.0 - - - +
315F PHE* 1.3 61.9 + - - +
334F GLY 3.2 22.3 - - - +
336F PRO* 3.4 26.2 - - + +
346F LEU* 4.1 33.0 - - + -
350F ILE* 4.1 11.4 - - + -
375F PHE* 5.9 0.2 - - + -
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Residues in contact with PHE 315 (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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65F TYR* 4.9 5.2 - + + -
68F ALA* 3.9 19.5 - - + -
71F LEU* 5.0 4.9 - - + -
72F CYS* 4.2 9.0 - - - -
203F SER 3.8 0.2 - - - +
204F TRP* 3.4 9.0 - - - +
205F VAL* 2.8 41.8 + - + +
207F VAL* 3.8 24.5 - - + -
295F LEU* 4.3 15.7 - - + -
302F ILE* 5.4 3.4 - - + -
313F GLN* 3.3 60.6 - - + -
314F LEU* 1.3 74.5 - - - +
316F GLY* 1.3 58.3 + - - +
317F PHE* 3.8 21.5 - + + -
332F VAL* 4.2 15.5 - - + -
333F ASN 3.4 11.9 - - - +
336F PRO* 3.8 4.9 - - - -
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Residues in contact with GLY 316 (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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202F ARG* 3.7 20.4 + - - -
203F SER 3.5 5.6 - - - -
204F TRP* 4.5 1.1 - - - -
315F PHE* 1.3 72.5 - - - +
317F PHE* 1.3 62.4 + - - -
318F ASP* 3.9 1.4 + - - +
331F GLU 3.9 1.0 - - - +
332F VAL* 3.5 2.3 - - - -
333F ASN* 2.8 43.7 + - - +
336F PRO* 3.7 13.0 - - - +
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Residues in contact with PHE 317 (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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71F LEU* 4.4 3.8 - - + -
201F ILE 3.4 1.4 - - - +
202F ARG* 3.3 5.5 - - - -
203F SER* 2.8 39.2 + - - +
205F VAL* 3.4 43.7 - - + -
290F ILE* 5.3 0.2 - - + -
291F ILE* 4.0 29.4 - - + -
294F CYS* 4.4 12.1 - - + -
295F LEU* 4.3 17.5 - - + -
315F PHE* 3.8 13.5 - - + -
316F GLY* 1.3 74.0 - - - -
318F ASP* 1.3 60.1 + - - +
319F PHE* 3.5 22.2 - + + -
329F LEU* 3.9 13.2 - - + -
331F GLU 3.8 1.8 - - - -
332F VAL* 3.6 35.2 - - + -
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Residues in contact with ASP 318 (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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200F ASP* 4.9 3.6 - - + +
201F ILE 3.4 3.8 - - - +
202F ARG* 2.6 36.6 + - - +
222F ARG* 3.2 18.6 + - - +
316F GLY 4.6 1.8 - - - -
317F PHE* 1.3 72.3 - - - +
319F PHE* 1.3 63.8 + - - +
329F LEU* 3.8 4.5 - - - +
330F ILE* 3.0 33.0 + - + -
331F GLU* 2.9 27.1 + - - +
333F ASN* 5.4 0.2 - - - +
401F ACP 3.0 41.5 + - + +
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Residues in contact with PHE 319 (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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200F ASP* 3.2 10.6 - - - +
201F ILE* 2.7 52.3 + - + +
203F SER* 4.2 7.6 - - - -
287F ILE* 3.4 42.0 - - + -
290F ILE* 3.8 24.9 - - + -
291F ILE* 4.2 9.2 - - + -
317F PHE* 3.5 34.8 - + + -
318F ASP* 1.3 76.3 - - - +
320F MET* 1.3 61.5 + - - +
327F VAL* 3.5 25.4 - - + -
328F TRP 3.2 12.3 - - - +
329F LEU* 3.8 17.0 - - + -
330F ILE* 4.3 2.0 - - - -
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Residues in contact with MET 320 (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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186F LEU* 3.6 22.4 - - + -
189F PRO* 3.9 21.8 - - + -
198F LYS* 3.9 16.4 - - + -
199F PHE 3.2 28.7 - - - +
200F ASP* 4.5 1.3 - - + -
319F PHE* 1.3 74.7 - - - +
321F VAL* 1.3 64.2 + - - +
322F ASP* 4.0 0.4 - - - -
326F LYS 3.5 2.1 - - - +
327F VAL* 3.5 1.3 - - - -
328F TRP* 2.8 39.0 + - + +
330F ILE* 3.7 28.2 - - + +
401F ACP 3.4 46.9 - - + +
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Residues in contact with VAL 321 (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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186F LEU* 6.1 0.2 - - - -
189F PRO* 4.1 5.0 - - - +
190F LEU* 3.0 25.7 + - + +
199F PHE* 4.0 19.7 + - + +
201F ILE* 3.5 32.1 - - + -
283F ILE* 3.7 37.9 - - + -
320F MET* 1.3 77.4 - - - +
322F ASP* 1.3 69.0 + - - +
325F LEU* 3.8 21.5 - - + -
326F LYS 3.4 7.2 - - - +
327F VAL* 4.3 6.5 - - + -
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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