Contacts of the helix formed by residues 3 - 16 (chain E) in PDB entry 5MNJ
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 LEU 3 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ALA* 1.3 78.3 - - - +
4E LYS* 1.3 59.4 + - + +
6E ILE* 3.8 5.4 - - + +
7E HIS* 2.8 35.6 + - + +
30E MET* 3.8 37.9 - - + -
31E PHE* 3.9 19.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 4 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ALA 3.4 0.8 - - - +
3E LEU* 1.3 78.8 - - + +
5E ARG* 1.3 58.4 + - - +
7E HIS* 3.7 6.6 + - - +
8E LYS* 2.9 27.9 + - - +
441G CYS 3.8 15.3 - - - +
442G GLN* 2.7 39.6 + - + +
443G GLY* 3.6 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ALA* 3.1 10.4 + - - +
4E LYS* 1.3 78.1 - - - +
6E ILE* 1.3 64.2 + - - +
8E LYS* 3.2 2.7 + - - +
9E GLU* 2.6 50.8 + - - +
60E TYR* 3.7 17.7 + - + -
61E PRO* 3.3 28.8 - - + +
95E PRO 2.9 28.8 + - - -
96E ALA* 4.4 1.4 - - - +
97E LEU 3.1 24.4 + - - -
98E THR* 3.9 8.8 - - - +
439G VAL* 2.7 41.4 + - - +
440G ILE* 3.7 15.0 - - - +
441G CYS 4.9 1.3 + - - +
442G GLN* 3.9 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 6 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ALA* 2.8 26.9 + - + +
3E LEU* 3.8 5.2 - - + +
5E ARG* 1.3 72.1 - - - +
7E HIS* 1.3 58.2 + - - +
9E GLU* 3.3 8.6 + - - +
10E LEU* 3.0 25.6 + - - +
30E MET* 3.6 25.6 - - + +
31E PHE* 3.7 43.7 - - + -
33E TRP* 3.5 25.7 - - + +
56E PHE* 3.8 24.5 - - + -
60E TYR* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 7 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LEU* 2.8 21.6 + - + +
4E LYS* 3.7 6.8 + - - +
6E ILE* 1.3 75.3 - - - +
8E LYS* 1.3 68.5 + - - +
10E LEU* 3.4 8.8 + - + +
11E ASN* 3.1 35.4 + - + +
30E MET* 4.1 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LYS 2.9 19.2 + - - +
5E ARG* 3.2 6.5 + - - +
7E HIS* 1.3 78.4 + - - +
9E GLU* 1.3 67.1 + - + +
11E ASN* 3.2 8.3 + - + +
12E ASP* 3.1 44.3 + - - +
436G GLU* 3.9 34.0 + - - +
437G PRO* 5.6 2.3 - - - +
442G GLN* 3.5 38.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ARG* 2.6 41.5 + - - +
6E ILE* 3.6 8.3 - - - +
8E LYS* 1.3 81.7 - - + +
10E LEU* 1.3 61.6 + - - +
12E ASP* 3.3 7.8 + - - +
13E LEU* 3.0 28.2 + - + +
33E TRP* 4.4 8.3 - - + -
56E PHE* 5.3 1.3 - - - -
60E TYR* 2.5 30.9 + - - -
98E THR* 3.3 21.8 - - + -
99E ILE* 2.8 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE 3.0 15.8 + - - +
7E HIS* 3.8 11.0 - - + +
8E LYS 3.3 0.2 - - - -
9E GLU* 1.3 76.1 - - - +
11E ASN* 1.3 57.5 + - - +
13E LEU* 3.4 3.8 + - + +
14E ALA* 2.8 32.9 + - + +
23E ALA 3.8 22.4 - - - +
24E GLY* 3.9 12.3 - - - -
25E PRO* 3.7 26.7 - - + -
30E MET* 4.3 15.3 - - + -
33E TRP* 3.8 14.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E HIS* 3.1 31.3 + - + +
8E LYS* 3.5 9.1 - - - +
9E GLU 3.2 0.2 - - - -
10E LEU* 1.3 77.1 - - - +
12E ASP* 1.3 65.1 + - - +
14E ALA* 3.6 6.8 + - - +
15E ARG* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LYS* 3.1 40.6 + - - +
9E GLU* 3.3 8.9 + - - +
11E ASN* 1.3 80.8 + - - +
13E LEU* 1.3 58.5 + - - +
15E ARG* 4.0 3.1 - - - +
16E ASP* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLU* 3.0 18.7 + - + +
10E LEU* 3.6 6.7 - - + +
12E ASP* 1.3 74.2 - - - +
14E ALA* 1.3 67.5 + - - +
15E ARG 3.1 0.9 + - - -
16E ASP 4.6 1.1 - - - +
17E PRO* 3.2 34.5 - - + +
18E PRO* 4.3 15.3 - - + -
21E CYS* 5.6 2.7 - - + -
22E ARG* 5.3 3.4 - - - -
23E ALA* 3.9 34.5 - - + +
33E TRP* 3.7 31.4 - - + -
99E ILE* 4.8 8.7 - - + -
100E SER* 4.0 27.6 - - - +
103E LEU* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 2.8 26.8 + - + +
11E ASN* 3.9 9.6 - - - +
13E LEU* 1.3 74.2 - - - +
15E ARG* 1.3 60.1 + - - +
17E PRO* 4.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASN* 3.1 19.5 + - - +
12E ASP* 4.0 3.6 - - - +
14E ALA* 1.3 80.0 - - - +
16E ASP* 1.3 62.0 + - + +
17E PRO* 3.8 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ASP 2.8 22.2 + - - +
13E LEU* 4.7 0.5 - - - +
15E ARG* 1.3 78.4 - - + +
17E PRO* 1.3 68.9 - - - +
18E PRO* 3.9 2.9 - - - +
6F LYS* 4.8 21.2 + - - +
----------------------------------------------------------
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