Contacts of the strand formed by residues 51 - 61 (chain G) in PDB entry 3M4D
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 LYS 51 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE 4.1 5.4 - - - +
44G ASP* 3.9 24.9 - - + +
50G LYS* 1.3 77.3 - - - +
52G LEU* 1.3 60.7 + - - +
233G THR* 3.4 4.9 - - - -
234G MET* 2.9 36.2 + - + +
236G ARG* 3.3 39.1 + - + +
241G GLN* 3.0 31.2 + - - +
286G TRP* 3.3 48.0 + - + +
287G GLU* 4.2 9.1 - - - +
289G GLU* 6.0 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 4.1 8.3 - - - +
5F ILE 5.7 0.9 - - - +
7F ILE* 4.4 16.6 - - + -
14G ILE* 3.6 39.5 - - + -
42G PHE* 3.5 5.2 - - - +
43G ILE* 2.9 47.1 + - + +
48G HIS* 4.0 11.4 - - + +
51G LYS* 1.3 77.3 - - - +
53G LEU* 1.3 62.5 + - - +
54G VAL* 4.3 0.9 - - + -
231G VAL* 3.5 23.6 - - + -
232G ILE 3.5 2.2 - - - +
233G THR* 3.2 33.9 - - + -
286G TRP* 3.8 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G TYR* 4.0 9.6 - - + -
41G SER 3.4 23.3 - - - +
42G PHE* 3.7 29.8 - - + -
52G LEU* 1.3 74.4 - - - +
54G VAL* 1.3 62.4 + - - +
55G ILE* 3.8 21.0 + - + -
230G THR 3.5 1.9 - - - +
231G VAL* 3.3 3.7 - - - -
232G ILE* 2.9 35.6 + - + +
284G ILE* 3.5 45.3 - - + -
286G TRP* 3.5 20.9 - - + -
291G MET* 4.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 4.1 15.7 - - + -
7F ILE* 3.6 30.3 - - + -
12F THR* 4.5 3.4 - - + -
39G PHE 3.7 1.2 - - - +
40G TYR* 3.2 6.1 - - - +
41G SER* 2.9 44.1 + - - +
43G ILE* 4.2 9.6 - - + -
52G LEU* 5.4 1.1 - - + -
53G LEU* 1.3 77.2 - - - +
55G ILE* 1.3 63.9 + - - +
56G ARG* 3.8 33.3 - - + +
229G ALA* 4.6 4.9 - - + -
230G THR 3.4 9.0 - - - +
231G VAL* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL* 3.8 24.0 - - + -
39G PHE 3.9 2.0 - - - -
40G TYR* 4.5 1.3 - - + +
53G LEU* 3.9 20.6 - - + +
54G VAL* 1.3 74.5 - - - +
56G ARG* 1.3 63.7 + - - +
57G THR* 3.9 11.3 + - + +
88G LEU* 4.0 20.9 - - + -
228G PHE 3.7 0.7 - - - +
229G ALA* 3.5 1.6 - - - -
230G THR* 2.8 40.1 + - - +
232G ILE* 3.7 28.5 - - + -
245G ILE* 3.8 14.8 - - + -
247G VAL* 5.6 1.1 - - + -
284G ILE* 4.5 0.9 - - + -
291G MET* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ASN* 3.5 27.2 - - - +
1F ALA* 4.9 10.1 - - - +
2F ASP* 3.4 19.8 + - - -
5F ILE* 4.7 6.9 - - - +
12F THR* 3.1 28.1 + - - +
37G LYS 3.6 0.5 - - - +
38G VAL* 3.4 5.4 - - - -
39G PHE* 2.8 56.3 + - + +
41G SER* 5.3 0.2 + - - -
54G VAL* 3.8 25.1 - - + +
55G ILE* 1.3 76.5 - - - +
57G THR* 1.3 61.6 + - - +
58G LYS* 3.7 12.6 + - + +
227G ASP* 5.0 9.3 + - - +
228G PHE 3.2 10.0 - - - +
229G ALA* 4.4 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LYS 3.6 2.9 - - - -
38G VAL* 4.8 5.4 - - + +
55G ILE* 4.3 8.7 - - + +
56G ARG* 1.3 72.1 - - - +
58G LYS* 1.3 59.6 + - - +
86G VAL* 3.6 25.2 - - + +
88G LEU* 4.2 25.6 - - + -
167G TRP* 4.9 1.7 - - - -
226G PRO* 3.4 9.2 - - - +
228G PHE* 2.9 42.5 + - - +
230G THR* 5.8 0.4 - - - +
247G VAL* 4.3 13.9 - - + -
249G TYR* 3.4 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ASP 3.1 19.0 + - - -
6E ASN* 2.9 24.5 + - - +
100F ASP* 2.8 29.7 + - - +
104F ARG* 3.4 14.3 - - - +
37G LYS* 2.8 38.9 + - - -
39G PHE* 4.8 0.9 - - + -
56G ARG* 4.3 18.2 - - + +
57G THR* 1.3 77.9 - - - +
59G GLY* 1.3 69.7 + - - +
226G PRO* 3.1 18.4 - - - +
227G ASP* 4.0 24.2 + - - +
249G TYR* 2.7 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F SER 5.3 1.1 + - - -
100F ASP* 5.7 1.6 + - - -
101F TYR* 3.2 15.9 + - - -
104F ARG* 5.4 0.2 - - - -
35G HIS* 3.2 18.2 - - - -
37G LYS* 4.0 10.1 - - - +
58G LYS* 1.3 84.1 - - - +
60G THR* 1.3 71.0 + - - +
225G SER* 3.2 18.7 - - - -
226G PRO* 3.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F TYR* 2.6 39.4 + - + +
157F LEU* 4.2 2.4 - - + +
160F PRO* 3.5 27.5 - - + +
33G GLY 4.3 0.2 - - - +
34G MET* 3.8 1.0 - - - -
35G HIS* 2.8 36.9 + - - +
58G LYS 3.9 0.2 + - - -
59G GLY* 1.3 69.3 - - - +
61G ILE* 1.3 71.5 + - - +
62G ALA* 3.8 2.3 + - - -
222G SER 4.5 6.2 + - - -
223G GLY 4.7 0.7 - - - -
224G PHE 3.3 12.2 + - - -
225G SER* 3.0 28.5 - - - +
226G PRO* 3.8 2.5 - - - -
249G TYR* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G GLY 4.0 2.7 - - - -
34G MET* 3.8 20.4 - - + -
60G THR* 1.3 73.2 - - - +
62G ALA* 1.3 69.5 + - - +
84G PHE* 3.7 29.8 - - + -
85G LYS 4.0 11.2 - - - +
86G VAL* 4.7 0.9 - - + -
223G GLY* 3.2 0.7 - - - -
224G PHE* 2.9 30.4 + - + +
226G PRO* 4.5 12.1 - - + -
249G TYR* 3.8 35.4 - - + -
250G GLU 3.8 17.7 - - - +
251G ARG* 3.5 27.6 - - + +
----------------------------------------------------------
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