Contacts of the strand formed by residues 63 - 68 (chain G) in PDB entry 6BA5
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 PHE 63 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G GLN* 4.1 9.0 - - - -
48G LEU* 4.2 22.7 - - + -
49G ILE* 3.9 6.4 - - + +
55G LEU* 3.6 24.6 - - + +
59G VAL* 4.0 10.5 - - + -
60G PRO* 3.1 34.6 + - + +
61G SER* 3.1 9.9 - - - +
62G ARG* 1.3 89.4 - - + +
64G SER* 1.3 60.3 + - - +
74G LEU* 4.4 11.9 - - + -
75G THR 3.5 2.5 - - - -
76G ILE* 3.7 26.0 - - + -
83G ASP* 3.7 27.6 - - - -
87G TYR* 3.7 33.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LYS* 4.3 21.0 + - - -
49G ILE* 3.9 7.9 - - - -
53G SER 5.9 0.2 - - - -
61G SER 4.9 2.2 - - - -
62G ARG 4.9 1.7 + - - -
63G PHE* 1.3 76.5 - - - +
65G GLY* 1.3 63.1 + - - +
73G THR 3.8 0.3 - - - +
74G LEU* 3.5 6.6 - - - +
75G THR* 2.9 48.1 + - - +
77G SER* 5.1 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TRP* 4.7 3.6 - - - -
49G ILE* 3.9 14.0 - - - +
52G ALA 3.3 20.4 - - - -
53G SER* 3.2 21.9 + - - +
64G SER* 1.3 78.0 - - - +
66G SER* 1.3 62.0 + - - -
73G THR 3.3 7.2 - - - -
74G LEU* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TRP* 5.4 0.3 + - - -
52G ALA* 3.8 6.3 + - - +
53G SER* 5.0 2.9 - - - -
65G GLY* 1.3 74.6 - - - -
67G ARG* 1.3 63.0 + - - +
72G TYR* 3.4 7.3 - - - +
73G THR* 2.9 47.4 + - - +
75G THR* 5.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 4.2 1.6 + - - -
32A SER* 4.0 8.1 + - - -
33A ASN* 5.2 0.6 + - - -
51A ARG* 5.4 3.6 + - - -
99B TYR* 3.3 54.8 + - - +
29G SER* 4.8 5.1 + - - -
31G ASP* 3.3 46.7 + - - +
32G SER* 3.5 15.9 + - - +
52G ALA* 4.4 8.5 - - + -
66G SER* 1.3 79.1 - - - +
68G SER* 1.3 63.8 - - - +
69G GLY* 3.2 22.9 + - - +
71G GLU 3.4 5.6 - - - +
72G TYR* 3.5 30.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 5.9 2.2 - - - +
99B TYR* 4.5 1.3 - - - -
67G ARG* 1.3 74.3 - - - +
69G GLY* 1.3 59.1 + - - +
70G THR 3.2 0.5 + - - -
71G GLU* 2.8 40.1 + - - +
333M GLN* 3.4 37.8 + - - +
----------------------------------------------------------
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