Contacts of the strand formed by residues 56 - 60 (chain G) in PDB entry 5GLF
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 THR 56 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G GLY 3.6 2.9 + - - -
55G ASP* 1.3 76.5 - - - +
57G VAL* 1.3 70.0 + - - +
68G VAL* 4.3 4.7 - - + -
69G CYS 3.3 10.5 - - - +
70G ILE* 4.8 2.9 - - - +
104G PRO* 4.0 1.7 - - - +
105G CYS* 3.0 37.4 + - + +
108G VAL* 3.9 23.8 - - + +
145G PRO* 4.1 20.8 - - + +
175G ILE* 3.9 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 4.1 15.9 - - + -
51G LEU* 3.8 28.3 - - + -
55G ASP 4.8 0.2 - - - -
56G THR* 1.3 79.9 - - - +
58G LEU* 1.3 61.4 + - - +
59G LEU* 4.0 7.1 + - + -
67G ALA 3.8 0.3 - - - +
68G VAL* 3.3 6.8 - - - +
69G CYS* 2.8 49.4 + - + +
71G VAL* 3.9 18.6 - - + -
102G ILE* 3.9 29.2 - - + -
103G GLN 3.4 9.9 - - - +
105G CYS* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G VAL* 1.3 72.5 - - - +
59G LEU* 1.3 66.3 + - - +
60G LYS* 4.2 4.9 - - - +
66G GLU* 3.8 41.1 - - + +
67G ALA 3.5 14.4 - - - +
68G VAL* 4.0 14.4 - - + -
101G SER 3.8 0.5 - - - +
102G ILE* 3.5 4.0 - - - -
103G GLN* 2.8 60.9 + - - +
104G PRO 4.8 2.0 - - - +
105G CYS* 3.6 20.9 - - + +
147G ARG* 5.5 0.7 - - - +
173G TYR* 5.0 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 3.8 15.7 - - + -
57G VAL* 4.1 9.4 - - + +
58G LEU* 1.3 76.1 - - - +
60G LYS* 1.3 63.3 + - - +
66G GLU* 3.2 7.6 - - - +
67G ALA* 2.7 38.6 + - + +
69G CYS* 3.7 29.6 - - + -
82G ILE* 4.1 9.9 - - + -
84G MET* 4.1 15.0 - - + -
88G VAL* 4.4 0.7 - - + -
92G LEU* 3.9 21.1 - - + -
100G ILE* 4.4 4.9 - - + -
101G SER 3.3 4.7 - - - +
102G ILE* 3.6 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ARG* 5.2 5.6 - - - +
58G LEU* 4.2 7.9 - - + +
59G LEU* 1.3 78.3 - - - +
61G GLY* 1.3 62.8 + - - +
65G ARG 3.6 4.5 - - - +
66G GLU* 3.5 30.5 - - + -
92G LEU* 4.3 1.6 - - - -
100G ILE* 3.3 8.6 - - - +
101G SER* 2.9 48.8 + - - +
103G GLN* 3.0 35.2 + - - +
----------------------------------------------------------
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