Contacts of the strand formed by residues 57 - 66 (chain X) in PDB entry 3RCK
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 LYS 57 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X ASP* 3.2 2.0 - - - -
54X ALA 2.9 37.9 + - - +
55X ASN* 4.0 14.8 - - + +
56X GLY* 1.3 81.5 - - - +
58X PRO* 1.3 72.3 - - + +
59X LEU* 3.4 5.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 58 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X VAL 3.8 1.6 - - - +
53X ASP* 3.2 15.9 - - - +
56X GLY 4.0 5.4 - - - +
57X LYS* 1.3 86.3 - - + +
59X LEU* 1.3 62.2 + - - +
60X GLY* 4.6 4.5 - - - +
183X LYS* 5.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X VAL* 2.8 26.7 + - + +
54X ALA* 3.9 34.8 - - + +
57X LYS* 4.2 6.3 - - + +
58X PRO* 1.3 73.5 - - - +
60X GLY* 1.3 57.1 + - - +
179X ASP* 5.0 0.3 - - - +
180X VAL* 3.4 17.9 - - + +
183X LYS* 2.6 52.1 + - + +
184X ILE* 3.9 28.7 - - + -
187X PHE* 4.1 18.8 - - + -
198X ILE* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X LEU 4.0 0.5 - - - +
51X ASP* 3.6 5.1 - - - +
52X VAL* 3.1 26.1 + - - +
58X PRO* 3.5 6.1 - - - +
59X LEU* 1.3 80.7 - - - +
61X ARG* 1.3 60.4 + - - -
180X VAL* 3.8 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X TYR* 3.5 41.2 - - + -
50X LEU 3.4 4.5 - - - +
51X ASP* 2.8 37.7 + - - +
60X GLY* 1.3 72.5 - - - -
62X VAL* 1.3 64.9 + - - +
63X VAL* 3.9 18.4 - - + -
176X GLU* 3.9 12.2 - - - +
177X GLY* 3.4 19.9 + - - -
180X VAL* 3.7 5.9 - - - +
202X ASP* 5.2 0.6 + - - -
206X LEU* 3.9 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X TYR* 3.2 5.0 - - - +
50X LEU* 2.8 49.8 + - + +
52X VAL* 4.6 8.3 - - + -
61X ARG* 1.3 72.6 - - - +
63X VAL* 1.3 61.1 + - - +
64X LEU* 4.0 27.3 + - + +
95X PHE* 6.1 0.7 - - + -
156X ILE* 4.2 8.3 - - + -
174X VAL* 4.2 4.9 - - + -
176X GLU 3.6 8.3 - - - +
177X GLY 4.0 0.7 - - - +
180X VAL* 3.7 30.1 - - + -
181X VAL* 4.0 26.9 - - + -
184X ILE* 5.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X LEU* 4.5 12.3 - - + -
48X VAL 3.4 10.1 - - - +
49X TYR* 4.5 0.4 - - + -
61X ARG* 3.9 24.5 - - + -
62X VAL* 1.3 76.5 - - - +
64X LEU* 1.3 64.5 + - - +
174X VAL* 3.5 6.2 - - - +
175X ILE* 2.8 46.0 + - + -
176X GLU* 2.9 39.2 + - + +
206X LEU* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X PRO 3.8 0.2 - - - +
47X LEU* 3.4 8.1 - - - +
48X VAL* 2.9 45.3 + - + +
50X LEU* 4.1 24.2 - - + -
62X VAL* 4.0 12.6 - - + +
63X VAL* 1.3 75.6 - - - +
65X GLU* 1.3 59.8 + - - +
66X LEU* 4.3 0.9 - - + -
78X PHE* 3.8 32.3 - - + -
140X LEU* 4.1 27.4 - - + -
154X PHE* 5.4 0.2 - - + -
156X ILE* 4.3 8.5 - - + -
173X HIS 3.3 11.7 - - - +
174X VAL* 3.7 30.1 - - + -
175X ILE* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X ASN* 2.9 37.4 + - + +
46X PRO 3.6 5.8 - - - +
47X LEU* 3.8 9.4 - - + +
64X LEU* 1.3 72.4 - - - +
66X LEU* 1.3 68.5 + - - +
67X LYS* 4.5 6.3 - - + -
172X GLY* 2.9 26.9 - - - -
173X HIS* 2.9 34.3 + - + +
175X ILE* 3.7 25.9 - - + +
212X 1FP 3.9 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X ASN* 3.1 18.9 - - - +
46X PRO* 3.0 24.6 + - + +
48X VAL* 3.7 32.5 - - + -
64X LEU* 4.3 1.3 - - + -
65X GLU* 1.3 76.0 - - - +
67X LYS* 1.3 59.5 + - - +
68X ALA 2.9 10.9 + - - -
75X ALA* 3.6 34.3 - - + +
78X PHE* 3.6 22.2 - - + -
79X ARG* 3.7 19.5 - - + +
140X LEU* 3.7 22.9 - - + -
171X PHE* 3.5 9.6 - - + +
----------------------------------------------------------
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