Contacts of the strand formed by residues 288 - 297 (chain A) in PDB entry 4Y05
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 LEU 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A ILE* 3.5 16.5 - - - +
284A PRO* 3.3 36.6 - - + +
285A SER* 3.1 18.8 + - - +
287A CYS* 1.3 82.3 - - - +
289A LEU* 1.3 60.0 + - - +
290A LEU* 4.6 11.2 - - + -
308A ALA* 4.4 13.0 - - + -
309A PHE 3.4 19.1 - - - +
310A CYS* 4.3 14.4 - - + -
314A ALA* 4.4 1.3 - - - -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A VAL* 3.6 32.1 - - + -
265A LYS* 5.4 0.2 - - + -
281A ILE* 3.8 17.3 - - + -
282A SER 3.6 4.3 - - - +
283A ILE* 4.1 11.9 - - + -
287A CYS 4.1 0.2 + - - -
288A LEU* 1.3 74.3 - - - +
290A LEU* 1.3 74.5 + - - +
291A VAL* 3.8 8.7 - - + -
307A GLN 3.7 0.3 - - - +
308A ALA* 3.4 3.1 - - - -
309A PHE* 2.8 39.0 + - + +
311A PHE* 4.4 6.7 - - + -
314A ALA* 4.8 0.2 - - + -
565A ILE* 3.5 27.1 - - + -
579A LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE* 3.6 35.9 - - + -
243A LEU* 4.4 8.3 - - + -
280A VAL 3.8 0.2 - - - +
281A ILE* 3.4 6.8 - - - -
282A SER* 2.7 37.4 + - - +
284A PRO* 4.0 25.4 - - + -
288A LEU* 4.6 11.9 - - + -
289A LEU* 1.3 83.1 - - - +
291A VAL* 1.3 59.3 + - - +
292A HIS* 4.1 12.1 + - + +
306A ASN* 5.0 7.2 - - + -
307A GLN 3.2 5.4 - - - +
308A ALA* 3.6 30.3 - - + +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A VAL* 3.5 7.9 - - + +
281A ILE* 4.0 13.0 - - + -
289A LEU* 3.8 10.1 - - + -
290A LEU* 1.3 70.8 - - - +
292A HIS* 1.3 66.5 + - - +
293A GLU* 3.8 7.0 + - + +
305A GLU 3.6 1.6 - - - +
306A ASN* 3.3 4.0 - - - -
307A GLN* 2.8 42.9 + - + +
309A PHE* 3.9 11.2 - - + -
572A CYS* 3.7 29.6 - - - -
575A THR* 4.6 2.0 - - + -
576A LEU* 4.0 15.9 - - + -
579A LEU* 3.5 31.9 - - + -
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PHE* 3.4 7.2 - - - -
236A ILE* 3.8 38.3 - - + +
239A PHE* 3.8 27.5 - + + -
240A ARG* 4.0 2.6 + - - +
280A VAL* 2.8 51.8 + - - +
282A SER* 2.7 33.9 + - - -
290A LEU* 4.3 9.2 - - + -
291A VAL* 1.3 71.6 - - - +
293A GLU* 1.3 62.0 + - - +
304A LEU* 3.7 13.8 - - + +
305A GLU 3.8 3.1 - - - -
306A ASN* 2.5 28.3 + - - -
572A CYS* 4.8 2.4 - - - -
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PHE* 3.4 9.7 - - - -
291A VAL* 4.3 10.8 - - + +
292A HIS* 1.3 74.8 - - - +
297A LYS* 1.3 65.0 + - - +
298A VAL* 3.9 3.3 + - + -
304A LEU* 3.6 1.1 - - - +
305A GLU* 2.8 46.7 + - + +
307A GLN* 3.3 36.3 - - - +
572A CYS* 4.3 10.3 - - - -
573A GLU* 4.9 2.8 - - - +
576A LEU* 3.7 21.3 - - - +
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Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASN* 5.0 13.2 + - + +
230A TRP* 4.4 26.2 - - + +
232A PHE* 3.3 39.8 - - + -
293A GLU* 1.3 72.4 - - - +
298A VAL* 1.4 64.4 + - - +
299A ASP* 3.4 41.2 + - + +
303A TYR 4.2 0.4 - - - -
569A ILE* 5.4 2.7 - - + -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLU* 4.4 5.4 - - + +
297A LYS* 1.4 77.3 - - - +
299A ASP* 1.4 53.1 + - - +
303A TYR* 3.1 33.4 + - - +
305A GLU* 3.4 46.2 - - + +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TRP* 4.2 34.9 + - + +
232A PHE* 4.8 3.1 - - - +
235A MET* 4.6 6.8 - - - +
297A LYS* 3.4 44.2 + - + +
298A VAL* 1.4 70.3 + - - +
303A TYR* 1.4 64.6 + - - +
304A LEU 4.1 0.5 + - - -
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A MET* 4.0 18.2 - - + -
297A LYS* 4.9 0.4 - - - -
298A VAL* 3.1 41.0 + - - +
299A ASP* 1.4 81.2 - - - +
304A LEU* 1.4 74.7 + - - +
305A GLU* 3.2 25.8 + - + -
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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