Contacts of the helix formed by residues 102 - 107 (chain N) in PDB entry 2QJK
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 102 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77M PHE* 3.8 31.9 - - + -
81M GLU* 3.8 40.8 - - + +
85M ARG* 4.4 1.3 - - - +
280M TYR* 3.6 28.3 - - + +
44N PHE* 4.1 10.8 - - + -
99N ASP 4.5 2.2 + - - -
100N LEU 3.2 0.2 - - - -
101N SER* 1.3 83.9 - - - +
103N MET* 1.3 67.4 + - - +
104N ALA 3.4 1.8 - - - -
105N LYS* 2.8 20.2 + - - +
106N ALA* 2.8 20.4 + - - -
219N ALA* 3.9 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 103 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281M ILE* 5.7 1.6 - - - -
98N PRO* 3.3 40.6 - - + -
99N ASP 3.9 8.0 + - - +
100N LEU* 3.3 39.9 + - + +
102N LEU* 1.3 74.7 - - - +
104N ALA* 1.3 54.8 + - - +
105N LYS 2.4 15.4 + - - -
106N ALA* 2.7 15.8 + - - +
107N ARG* 3.2 49.2 + - + +
131N ILE* 4.0 20.2 - - + -
215N LEU* 5.7 1.6 - - + -
301N HEM 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N LEU 5.1 0.2 + - - -
102N LEU 3.3 1.4 + - - -
103N MET* 1.3 74.8 - - - +
105N LYS* 1.3 62.1 + - - +
107N ARG 4.5 0.3 - - - +
125N ILE* 6.0 1.2 - - - +
127N GLY* 3.8 22.1 + - - -
128N PRO* 4.0 13.0 - - + +
131N ILE* 3.7 20.5 - - + +
215N LEU* 3.8 22.5 + - - +
216N MET* 3.8 27.8 - - - +
219N ALA* 4.7 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M GLU* 4.9 2.8 + - - -
84M MET* 3.9 10.5 - - - +
95M TYR* 2.9 22.6 + - - +
272M ASN* 3.4 18.2 - - + +
277M PRO* 3.6 17.8 - - - +
280M TYR* 3.3 48.3 + - + -
102N LEU* 2.8 16.3 + - + +
103N MET 2.4 12.3 + - - -
104N ALA* 1.3 73.2 - - - +
106N ALA* 1.3 60.6 + - - +
107N ARG 3.0 11.0 + - - +
125N ILE* 4.9 3.5 - - - +
216N MET* 5.7 4.3 - - + -
219N ALA* 3.8 19.1 + - + -
220N GLU* 3.6 28.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M PRO* 3.2 31.0 - - - +
278M ASP* 4.0 7.4 - - - +
280M TYR* 4.1 8.4 - - + +
281M ILE* 3.8 18.1 - - + +
102N LEU 2.8 13.4 + - - +
103N MET* 2.7 11.8 + - - +
105N LYS* 1.3 77.9 - - - +
107N ARG* 1.3 85.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M PRO* 4.5 2.0 - - - -
278M ASP* 5.8 0.7 - - - -
281M ILE* 3.5 19.1 - - - +
98N PRO* 5.7 3.2 - - - +
103N MET* 3.2 32.1 + - + +
104N ALA 4.5 0.5 - - - +
105N LYS 3.0 5.4 - - - +
106N ALA* 1.3 107.7 + - - +
108N ALA* 1.3 61.8 + - - +
125N ILE* 3.3 16.0 - - - +
127N GLY* 3.4 20.5 - - - -
130N TYR* 3.9 34.9 + - + -
131N ILE* 6.0 0.2 - - + -
162N ASN* 5.2 8.2 - - - +
301N HEM 3.3 35.4 + - - +
----------------------------------------------------------
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