Contacts of the strand formed by residues 56 - 61 (chain C) in PDB entry 3RMD
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 56 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C HIS* 3.6 7.8 - - - +
41C CYS* 3.1 45.9 + - - +
43C GLU* 4.5 26.9 - - + +
45C GLN 4.9 4.5 - - - +
46C ALA* 6.4 0.2 - - - -
47C THR* 4.8 3.8 - - - +
49C TYR 3.5 1.1 - - - +
50C PHE* 3.5 27.1 - - + -
54C GLY 3.6 6.0 - - - +
55C LYS* 1.3 90.2 - - + +
57C CYS* 1.3 60.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.9 20.9 - - + -
39C ALA 3.1 13.7 - - - +
40C HIS* 4.7 5.8 - - - -
41C CYS* 3.6 5.8 - - - -
47C THR* 2.7 23.2 + - - -
49C TYR* 2.9 19.8 + - - +
50C PHE 4.2 2.5 - - - -
51C ASP* 3.8 26.2 - - - -
55C LYS 3.6 12.1 - - - -
56C PRO* 1.3 79.3 - - - +
58C THR* 1.3 59.0 + - - +
59C ARG 4.2 0.2 + - - -
83C LEU* 4.6 11.9 - - - -
379C VAL* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.3 7.8 - - - -
39C ALA* 2.8 34.0 + - + +
40C HIS 4.1 3.1 - - - +
41C CYS* 3.1 34.3 - - + -
45C GLN* 4.1 15.9 - - - +
47C THR* 4.7 9.0 - - - -
57C CYS* 1.3 73.6 - - - +
59C ARG* 1.3 63.3 + - - +
60C LYS* 3.5 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 3.2 38.3 + - - -
37C LEU 3.7 3.8 - - - -
38C PHE* 3.4 20.0 - - + -
47C THR* 5.5 1.2 - - - +
49C TYR* 3.1 50.8 + - + -
58C THR* 1.3 73.7 + - - +
60C LYS* 1.3 62.1 + - - +
61C LEU* 4.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 3.2 2.2 - - - -
37C LEU 2.7 43.3 + - - +
39C ALA* 4.5 11.2 - - + +
58C THR* 3.8 18.4 - - - +
59C ARG* 1.3 76.9 - - - +
61C LEU* 1.3 59.4 + - - +
62C PHE* 3.1 19.4 - - + -
71C TRP* 3.0 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LYS* 3.4 34.5 - - + +
35C PRO 3.7 3.6 - - - +
36C SER* 3.6 17.5 - - - +
59C ARG* 4.0 26.4 + - - +
60C LYS* 1.3 70.4 - - - +
62C PHE* 1.3 94.7 + - - +
----------------------------------------------------------
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