Contacts of the strand formed by residues 50 - 56 (chain E) in PDB entry 4GG6
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 PRO 50 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 4.8 6.7 - - + -
43E ARG 3.1 13.5 - - - +
44E GLN* 3.7 17.7 - - + +
49E GLY* 1.3 88.2 - - - +
51E GLU* 1.3 61.0 - - - +
103E TYR* 4.9 3.4 - - + -
118E PHE* 5.6 0.7 - - + -
50F LEU* 3.6 31.2 - - + -
103F PHE* 4.3 8.3 - - + -
118F PHE* 3.3 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 3.4 8.3 - - - -
43E ARG* 2.7 83.4 + - + +
44E GLN* 5.7 0.4 - - - -
45E LEU* 5.9 2.9 - - + +
48E GLN* 4.8 9.2 - - - +
49E GLY 4.7 5.7 - - - +
50E PRO* 1.3 77.1 - - - +
52E TYR* 1.3 69.3 + - - +
53E VAL 3.5 0.2 + - - -
75E MET* 5.4 6.5 - - - +
116F GLN 4.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E HIS* 4.6 3.1 - + - -
42E TYR* 3.5 37.1 - + + -
51E GLU* 1.3 76.7 - - - +
53E VAL* 1.3 74.0 + - - +
54E ILE* 3.3 24.1 - - - +
55E HIS* 2.5 49.3 + + + -
68E ASN* 3.9 10.4 + - - -
75E MET* 3.4 30.6 - - + +
115F GLU* 3.4 56.8 + - + +
116F GLN 4.4 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TRP* 2.9 26.6 + - + +
42E TYR 4.0 2.5 - - - -
43E ARG* 3.8 39.0 - - + +
51E GLU 3.9 0.9 - - - +
52E TYR* 1.3 83.5 - - - +
54E ILE* 1.3 52.5 + - - +
68E ASN* 2.7 31.4 + - - +
75E MET* 3.9 18.1 - - + +
76E ALA* 3.7 28.9 - - + -
89E LEU* 4.1 14.1 - - + -
91E LEU* 4.9 4.5 - - + -
102E TYR* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TRP* 3.0 31.7 + - + +
52E TYR* 3.3 15.8 - - - +
53E VAL* 1.3 81.3 - - + +
55E HIS* 1.3 64.5 + - - +
66E VAL* 3.3 43.3 - - + +
67E ASN* 3.9 0.4 - - - -
68E ASN* 3.4 17.5 - - - +
76E ALA 3.4 23.6 - - - +
78E LEU* 3.7 26.9 - - + +
89E LEU* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D GLU* 5.0 14.2 + - + +
38E TYR* 3.6 28.2 - + - -
39E ILE 3.0 13.0 - - - +
40E HIS* 3.5 24.9 - + + +
52E TYR* 2.5 36.0 + + + +
54E ILE* 1.3 77.2 - - - +
56E GLY* 1.3 57.5 - - - +
66E VAL* 3.7 19.2 - - - +
78E LEU* 4.0 7.0 - - - -
113F THR* 3.1 41.2 + - - -
114F TYR* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E TYR* 3.3 12.8 - - - -
39E ILE* 2.7 39.1 + - - +
55E HIS* 1.3 77.0 - - - +
57E LEU* 1.3 59.7 + - - -
66E VAL* 3.9 17.5 - - - -
78E LEU* 3.7 7.0 - - - +
80E ILE* 4.0 5.2 - - - -
----------------------------------------------------------
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