Contacts of the strand formed by residues 19 - 24 (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 VAL 19 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E MET* 4.8 6.1 - - + -
13E SER* 3.6 27.4 - - - -
17E GLU 3.8 1.3 - - - +
18E PRO* 1.3 76.1 - - - +
20E HIS* 1.3 69.8 + - - +
21E LEU* 4.0 17.5 - - + -
89E LEU 3.4 2.1 - - - +
90E ILE* 3.3 6.8 - - - +
91E LEU* 3.0 40.7 + - + +
94E ALA* 3.8 26.7 - - + -
124E LEU* 3.9 26.0 - - + -
126E ILE* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E MET* 3.8 10.4 - - - +
18E PRO* 4.3 19.3 + - + -
19E VAL* 1.3 77.6 + - - +
21E LEU* 1.3 63.7 + - - +
22E PRO* 3.6 8.3 - - - +
88E THR* 3.6 16.4 - - + -
89E LEU 3.5 3.8 - - - -
90E ILE* 3.7 39.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E MET* 3.7 22.0 - - + -
19E VAL* 4.2 6.5 - - + -
20E HIS* 1.3 73.7 - - - +
22E PRO* 1.3 65.4 - - + +
41E TRP* 3.7 16.1 - - + -
88E THR* 3.3 6.2 - - - -
89E LEU* 2.8 63.8 + - + +
91E LEU* 4.5 6.7 - - + -
102E TYR* 3.7 27.4 - - + -
122E THR* 4.4 17.5 - - + -
124E LEU* 4.2 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 3.8 7.1 + - - +
8E PRO* 3.4 37.3 - - + +
11E MET* 3.7 21.3 - - + -
20E HIS 3.6 8.5 - - - +
21E LEU* 1.3 87.2 - - + +
23E CYS* 1.3 62.7 + - - +
24E ASN* 6.0 0.9 - - - +
41E TRP* 3.8 3.5 - - - -
87E SER 3.7 5.6 - - - +
88E THR* 4.8 4.5 - - + +
122E THR* 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E THR* 3.9 8.5 - - - -
5E THR 3.6 5.6 - - - -
6E GLN* 4.1 3.8 - - + -
22E PRO* 1.3 77.2 - - - +
24E ASN* 1.3 73.1 + - - +
25E HIS* 3.6 14.1 + - - -
41E TRP* 3.3 15.0 - - + -
86E SER* 3.3 5.2 - - - -
87E SER* 3.0 34.0 + - - +
104E CYS* 2.0 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E THR* 3.2 7.3 - - - -
5E THR* 2.8 51.8 + - - +
22E PRO* 6.0 0.5 - - - +
23E CYS* 1.3 77.5 - - - +
25E HIS* 1.3 67.3 + - - +
26E SER* 5.2 5.6 - - - +
85E LYS 3.9 3.4 - - - +
86E SER* 3.4 16.3 - - - -
----------------------------------------------------------
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