Contacts of the strand formed by residues 313 - 317 (chain A) in PDB entry 3BYU
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 TYR 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ARG* 3.2 46.2 + - + +
245A LEU* 4.1 9.0 - - + -
247A LEU* 3.3 39.8 - - + +
272A VAL* 3.7 15.7 - - + -
273A LYS 3.2 2.9 - - - -
274A SER* 3.4 33.4 - - - -
306A VAL* 3.4 5.7 - - - +
307A VAL* 3.0 43.3 + - + +
311A PRO* 3.5 16.7 + - + +
312A ILE* 1.3 77.0 - - - +
314A ILE* 1.3 69.9 + - - +
315A ILE* 3.8 13.2 - - + -
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A AM6 3.9 26.8 - - + -
271A ALA 3.9 0.2 - - - +
272A VAL* 3.5 2.1 - - - -
273A LYS* 2.9 34.5 + - + +
285A PHE* 3.6 39.3 - - + +
286A LEU* 4.5 4.0 - - + -
288A GLU* 3.6 23.6 - - - +
289A ALA* 4.1 19.3 - - + +
292A MET* 4.7 2.0 - - - -
303A LEU* 3.9 23.6 - - + -
305A ALA 3.8 4.5 - - - +
306A VAL* 4.2 6.7 - - + -
313A TYR* 1.3 79.5 - - - +
315A ILE* 1.3 63.6 + - - +
316A THR* 4.6 0.2 - - + -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 4.7 1.6 - - + -
245A LEU* 3.4 37.5 - - + -
264A TYR* 5.9 0.7 - - + -
270A VAL* 3.6 29.6 - - + -
271A ALA 3.3 11.2 - - - +
272A VAL* 4.1 9.0 - - + -
303A LEU* 3.8 2.1 - - - +
304A TYR* 2.7 37.4 + - + +
305A ALA* 2.8 40.6 + - + +
306A VAL* 3.9 9.0 - - - +
307A VAL* 4.3 1.6 - - + -
313A TYR* 3.8 15.9 - - + -
314A ILE* 1.3 78.2 - - - +
316A THR* 1.3 63.4 + - - +
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Residues in contact with THR 316 (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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1A AM6 3.2 54.2 + - + -
270A VAL* 3.6 9.5 - - - +
271A ALA* 2.9 29.8 + - - +
292A MET* 3.9 15.5 - - + -
301A VAL* 3.6 9.2 - - + +
302A ARG 3.2 15.9 - - - +
303A LEU* 4.4 0.9 - - - -
304A TYR* 3.7 8.8 - - - +
314A ILE* 4.6 2.2 - - + -
315A ILE* 1.3 78.0 - - - +
317A GLU* 1.3 70.6 + - - +
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Residues in contact with GLU 317 (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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1A AM6 3.2 13.2 - - - -
271A ALA* 3.7 0.9 - - - +
300A LEU 3.6 5.2 - - - +
301A VAL* 3.6 8.1 - - + +
302A ARG* 2.7 44.5 + - - +
304A TYR* 3.2 34.1 + - + +
316A THR* 1.3 91.1 + - - +
318A TYR* 1.3 59.2 + - - +
319A MET* 4.7 11.4 - - + +
379A LYS* 2.8 36.6 + - - -
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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