Contacts of the helix formed by residues 51 - 61 (chain B) in PDB entry 4F2N
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 SER 51 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY* 3.7 3.4 - - - -
47B GLN* 4.0 4.3 - - - +
49B VAL 4.1 0.8 + - - -
50B MET* 1.3 74.8 - - - +
52B PRO* 1.4 76.1 - - - +
53B ARG* 3.6 6.2 + - - +
54B GLN 3.0 15.4 + - - -
55B LEU 3.0 18.4 + - - -
199B LYS* 4.5 1.2 - - - +
200B ASP* 2.7 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR 4.8 3.1 - - - +
43B LYS* 3.4 26.1 - - - +
44B ASP* 3.8 10.1 - - - +
45B GLY* 3.7 11.6 - - - +
47B GLN* 4.0 11.9 - - - +
51B SER* 1.4 87.6 - - - +
53B ARG* 1.3 57.9 + - - +
55B LEU* 3.3 3.3 + - - +
56B GLU* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 2.8 36.5 + - - +
51B SER* 3.3 5.3 + - - +
52B PRO* 1.3 75.7 - - - +
54B GLN* 1.3 66.0 + - - +
56B GLU* 3.0 35.4 + - - +
57B LEU* 3.0 39.9 + - + +
61B LYS* 4.6 10.9 - - - +
199B LYS* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 4.9 1.8 + - - -
50B MET* 4.3 15.5 - - + -
51B SER* 3.0 15.5 + - - +
53B ARG* 1.3 75.9 - - - +
55B LEU* 1.3 63.2 + - - +
57B LEU* 3.6 6.8 + - - +
58B HIS* 3.1 21.7 + - + +
195B HIS 3.1 23.2 + - - -
196B ALA* 3.3 16.1 + - - +
197B TYR* 3.1 15.8 - - - -
199B LYS* 3.1 38.4 + - + +
200B ASP* 3.3 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.3 6.7 - - + -
40B PHE* 3.9 16.8 - - + -
42B TYR* 3.4 31.2 - - + +
45B GLY* 3.6 25.4 - - - +
46B ILE* 4.0 12.1 - - + -
50B MET* 4.7 8.3 - - + +
51B SER 3.0 12.4 + - - +
52B PRO 3.8 6.1 - - - +
54B GLN* 1.3 76.2 - - - +
56B GLU* 1.3 61.5 + - - +
58B HIS* 4.4 1.8 - - - -
59B TYR* 2.8 40.5 + - + +
112B TRP* 3.7 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 5.5 3.1 + - - +
52B PRO 2.8 18.0 + - - +
53B ARG* 3.0 39.9 + - - +
55B LEU* 1.3 74.8 - - - +
57B LEU* 1.3 61.3 + - - +
59B TYR* 5.1 0.9 - - - -
60B SER* 2.8 49.7 + - - +
61B LYS* 3.4 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 3.7 28.3 - - + +
202A GLU* 3.6 32.8 - - + +
203A ASN* 3.7 24.0 - - - +
53B ARG* 3.0 50.2 + - - +
54B GLN* 3.8 5.4 - - - +
56B GLU* 1.3 74.7 - - - +
58B HIS* 1.3 64.2 + - - +
61B LYS* 3.0 29.9 + - + +
62B HIS* 3.0 13.2 + - + -
199B LYS* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 5.3 4.2 - - - +
54B GLN* 3.1 20.5 + - + +
55B LEU* 3.8 4.7 - - - +
57B LEU* 1.3 80.1 - - - +
59B TYR* 1.3 58.9 + - - +
62B HIS* 3.3 8.2 - - + +
63B HIS* 2.9 26.7 + - - +
108B HIS* 3.1 20.1 + + - -
111B PHE* 4.1 15.3 - + - -
112B TRP* 3.6 17.8 - + + -
191B ASP* 2.8 30.7 + - - -
195B HIS* 3.0 24.9 + + - +
196B ALA* 3.5 30.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.7 40.9 + - + +
36B PRO* 2.6 32.9 + - + -
37B THR* 4.5 2.4 - - - -
38B LEU* 3.5 35.0 + - + +
42B TYR* 4.9 13.5 - - + -
55B LEU* 2.8 23.0 + - + +
56B GLU* 5.1 0.7 - - - -
58B HIS* 1.3 77.3 - - - +
60B SER* 1.3 72.6 + - - +
61B LYS 3.4 0.2 - - - -
63B HIS* 3.4 5.2 - - - +
64B SER 3.1 24.9 + - - -
112B TRP* 3.7 32.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.9 3.5 - - - +
42B TYR* 6.0 0.7 - - - +
56B GLU* 2.8 36.1 + - - +
59B TYR* 1.3 88.4 - - - +
61B LYS* 1.3 66.9 + - - +
64B SER* 3.1 19.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASN* 3.6 39.5 - - + +
53B ARG* 4.6 13.6 - - - +
56B GLU* 4.7 15.0 + - - -
57B LEU* 3.0 38.0 + - + +
60B SER* 1.3 87.5 + - - +
62B HIS* 1.3 66.2 + - - +
63B HIS 3.6 0.2 - - - -
64B SER* 4.0 0.3 - - - -
65B ALA* 3.1 25.3 + - - +
----------------------------------------------------------
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