Contacts of the strand formed by residues 40 - 45 (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 GLY 40 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 3.9 14.8 - - - +
33H LEU 3.1 12.6 - - - -
34H ILE* 3.6 9.8 - - - +
39H GLU* 1.3 75.4 - - - +
41H PHE* 1.3 67.0 + - - +
67H ARG* 5.5 2.0 - - - +
151H GLN* 4.6 9.0 - - - +
399I ARG* 3.6 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 4.1 2.2 - - - +
33H LEU* 3.2 22.1 + - + -
34H ILE* 3.5 28.5 - - - -
35H ASN* 3.7 4.0 - - + -
39H GLU* 3.2 19.1 - - + -
40H GLY* 1.3 74.3 - - - +
42H CYS* 1.3 86.8 + - + +
58H CYS 4.2 7.9 - - - -
59H LEU* 5.2 0.9 - - + -
61H ALA* 4.9 3.6 - - + -
64H PHE* 3.9 23.3 - + + -
151H GLN* 5.3 0.2 - - - +
193H GLY 4.1 8.8 + - - +
394I SER* 4.0 1.2 - - - -
395I LEU* 3.1 46.0 + - + -
397I PRO* 4.1 47.8 - - + -
399I ARG* 4.5 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 4.0 4.4 - - - +
33H LEU* 3.1 45.0 + - + +
41H PHE* 1.3 101.6 - - + +
43H GLY* 1.3 65.6 + - - +
58H CYS* 2.0 50.7 - - - -
193H GLY 4.0 5.0 + - - -
195H ALA 3.3 4.7 - - - -
394I SER* 3.4 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H GLN* 3.6 17.5 - - - -
31H ALA 3.8 2.9 - - - -
32H LEU* 4.9 2.7 - - - -
33H LEU* 4.9 0.4 - - - -
42H CYS* 1.3 73.8 - - - +
44H GLY* 1.3 56.1 + - - -
54H THR* 3.0 15.1 + - - -
140H GLY* 5.8 1.8 - - - -
141H PHE* 6.6 0.2 - - - -
193H GLY 4.1 5.6 + - - -
194H ASP* 4.0 4.2 + - - -
195H ALA 2.8 9.9 + - - -
196H GLY* 2.5 28.0 - - - +
197H GLY* 3.5 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ALA* 3.2 35.8 + - - -
32H LEU 4.8 0.4 - - - -
33H LEU* 5.4 2.5 - - - -
42H CYS 3.7 0.2 + - - -
43H GLY* 1.3 75.3 - - - -
45H THR* 1.3 63.3 + - - -
52H ILE* 4.1 8.5 - - - -
53H LEU 3.4 8.7 - - - -
54H THR* 4.6 1.1 - - - -
196H GLY 3.7 0.2 - - - -
198H PRO* 3.0 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H TRP* 3.6 5.6 - - + -
31H ALA* 3.8 1.8 - - - +
44H GLY* 1.3 77.8 + - - -
46H ILE* 1.3 70.8 + - - +
47H LEU* 2.9 14.0 + - + +
52H ILE* 4.1 0.9 - - - +
53H LEU* 3.0 45.3 + - - +
121H ALA* 4.5 10.5 - - + -
196H GLY 3.9 0.5 + - - -
197H GLY 3.9 2.4 + - - -
198H PRO* 3.4 32.6 - - + +
209H VAL* 4.2 24.6 - - + +
212H ILE* 5.6 1.9 - - - +
----------------------------------------------------------
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