Contacts of the strand formed by residues 64 - 68 (chain H) in PDB entry 2GD4
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 64 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LEU* 4.2 26.7 - - + -
34H ILE 2.9 15.5 - - - +
35H ASN* 4.2 1.8 - - - +
36H GLU* 5.0 0.7 - - - +
41H PHE* 3.9 18.4 - + + -
59H LEU* 3.5 34.8 - - + -
61H ALA* 5.4 7.4 - - + -
62H LYS 4.9 1.1 - - - -
63H ARG* 1.3 90.3 - - - +
65H LYS* 1.3 77.8 + - - +
85H VAL* 4.2 27.5 + - + +
88H VAL* 3.7 30.5 - - + -
106H LEU* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU 3.5 0.2 - - - +
33H LEU* 3.2 4.5 - - - -
34H ILE* 2.7 42.9 + - + +
35H ASN 5.6 4.3 - - - +
36H GLU* 4.4 18.4 - - - +
64H PHE* 1.3 89.7 - - - +
66H VAL* 1.3 65.0 + - - +
82H VAL* 4.0 24.0 - - + +
83H HIS 3.6 13.5 - - - +
84H GLU* 4.5 26.7 + - + +
85H VAL* 4.8 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ALA* 4.1 20.9 - - + -
32H LEU 3.2 7.4 - - - +
33H LEU* 3.4 28.0 - - + -
52H ILE* 4.2 14.4 - - + -
65H LYS* 1.3 76.0 - - - +
67H ARG* 1.3 70.7 + - - +
68H VAL* 4.1 8.0 + - + -
81H ALA 3.7 0.5 - - - +
82H VAL* 3.5 3.3 - - - -
83H HIS* 2.8 36.2 + - + +
85H VAL* 4.4 4.7 - - + -
106H LEU* 3.9 15.9 - - + -
108H LEU* 4.3 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ALA* 3.8 1.0 - - - -
32H LEU* 2.7 59.8 + - + +
34H ILE* 3.7 28.3 - - + +
38H ASN* 3.2 32.9 + - - +
39H GLU* 6.1 0.2 - - - +
40H GLY 5.5 2.2 - - - +
65H LYS 4.1 0.4 + - - -
66H VAL* 1.3 75.3 - - - +
68H VAL* 1.3 67.4 + - - +
70H ASP* 3.6 28.0 + - + +
73H THR* 4.5 18.0 + - - +
80H GLU* 4.3 16.6 + - + -
81H ALA 3.1 16.6 - - - +
82H VAL* 4.1 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H GLN 4.8 2.2 - - - -
31H ALA* 4.7 2.0 - - + -
46H ILE* 3.4 28.9 - - + -
52H ILE* 5.1 0.7 - - + -
66H VAL* 4.3 14.4 - - + -
67H ARG* 1.3 77.8 - - - +
69H GLY* 1.3 68.8 + - - +
70H ASP* 2.9 6.9 + - - +
80H GLU* 3.6 2.9 - - - -
81H ALA* 2.8 54.6 + - + +
83H HIS* 3.9 20.0 - - + +
108H LEU* 6.0 0.2 - - + -
112H ILE* 4.1 9.2 - - + -
118H VAL* 3.8 20.2 - - + -
----------------------------------------------------------
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