Contacts of the strand formed by residues 287 - 292 (chain 5) in PDB entry 3J7Y
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 287 (chain 5).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2295 ARG* 4.3 0.7 - - - -
2325 THR* 2.8 53.7 + - - +
2335 LYS 3.9 10.1 - - - +
2345 ASP 3.8 15.0 - - - +
2355 PRO* 3.5 36.1 - - + -
2855 TYR 3.4 0.4 - - - -
2865 PRO* 1.3 97.7 - - + +
2885 PRO* 1.4 64.9 - - + +
3245 GLN* 3.5 22.3 + - + -
3275 LEU* 5.2 10.6 - - + +
3285 LEU* 4.6 22.0 - - + +
3405 VAL* 6.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 288 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2295 ARG* 3.3 26.0 - - - +
2305 LEU 3.8 5.4 - - - +
2315 SER* 4.6 0.2 - - - -
2365 LEU* 5.2 1.0 - - - +
2865 PRO 3.5 5.1 - - - +
2875 TYR* 1.4 81.9 - - + +
2895 HIS* 1.3 65.9 + - - +
2915 LEU* 4.7 9.0 - - + -
3205 SER* 4.7 7.9 - - - -
3245 GLN* 3.4 37.9 - - + +
3415 VAL 3.8 15.1 - - - +
3425 VAL* 3.9 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 289 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2015 ARG* 3.1 25.7 + - - -
2305 LEU* 2.8 33.6 + - + +
2325 THR* 3.5 22.0 - - + +
2365 LEU* 3.6 22.1 - - + +
2875 TYR 3.2 2.2 + - - -
2885 PRO* 1.3 74.8 - - - +
2905 THR* 1.3 68.2 + - - +
3425 VAL* 3.8 1.5 - - - -
3435 GLN* 2.8 39.2 + - - +
4175 LEU 3.1 21.0 + - - -
4185 TYR* 3.0 20.4 + - - -
4205 HIS* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2305 LEU* 2.8 34.4 + - - +
2885 PRO 3.8 0.2 - - - -
2895 HIS* 1.3 94.6 + - - +
2915 LEU* 1.3 65.1 + - - +
2925 TYR* 3.2 41.3 + - + +
3435 GLN* 3.2 34.3 + - + +
3455 VAL* 3.8 20.2 - - + +
4175 LEU* 5.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2075 SER* 5.6 0.4 - - - +
2095 PHE* 4.4 11.2 - - + -
2255 SER* 3.8 23.1 - - - +
2285 ALA 3.6 4.7 - - - +
2295 ARG* 4.2 29.8 - - + +
2885 PRO* 4.7 6.5 - - + -
2905 THR* 1.3 69.6 - - - +
2925 TYR* 1.3 61.1 + - - +
2935 LEU* 3.1 18.0 + - + +
3165 PHE* 4.5 17.5 - - + +
3205 SER* 4.0 17.5 - - - +
3425 VAL* 3.9 23.8 - - + -
3435 GLN 2.8 8.9 + - - -
3445 SER* 3.3 18.6 - - - -
3455 VAL 3.2 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1815 VAL* 4.8 5.6 - - + -
1855 ILE* 3.8 36.1 - - + -
2035 CYS* 5.0 4.3 - - + -
2275 GLY* 4.1 0.2 - - - -
2285 ALA* 2.8 46.4 + - + +
2305 LEU* 3.5 42.4 - - + +
2905 THR* 3.2 26.7 + - + +
2915 LEU* 1.3 67.4 - - - +
2935 LEU* 1.3 62.6 + - - +
2945 LEU* 4.3 6.5 - - - +
3455 VAL* 3.4 31.0 - - + -
4145 PHE* 4.2 16.8 + + - -
4175 LEU* 5.3 2.2 - - + +
4185 TYR* 3.4 32.7 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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