Contacts of the helix formed by residues 118 - 126 (chain F) in PDB entry 6N1H
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 HIS 118 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F PHE* 3.3 52.8 + + - +
115F ILE 4.0 3.8 - - - -
116F ASP 3.4 0.2 - - - -
117F GLN* 1.3 100.3 + - + +
119F ARG* 1.3 56.9 + - - +
120F ALA 3.3 2.5 - - - -
121F ALA* 3.2 9.4 + - + +
122F LEU* 2.9 30.5 + - + +
192F LEU* 3.3 55.2 + - + +
193F GLU* 5.2 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP* 3.9 9.1 + - - -
137C TYR* 3.2 56.0 + - + -
143C ASP* 5.4 1.2 + - - -
146C TYR* 3.3 38.0 + - - -
115F ILE 3.8 10.0 + - - +
116F ASP* 3.9 16.8 - - - +
117F GLN 3.4 4.4 + - - -
118F HIS* 1.3 76.5 - - - +
120F ALA* 1.3 63.8 + - - +
122F LEU 3.7 0.2 + - - -
123F ILE* 3.3 48.6 + - - +
160F ARG* 4.6 6.3 + - - +
163F PHE* 3.7 52.0 + - + +
164F SER* 5.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TRP* 5.2 9.0 + - + +
134C ASP* 3.8 38.9 + - + +
135C ALA* 4.8 3.6 - - - +
117F GLN 5.2 0.2 + - - -
118F HIS 3.3 0.6 - - - -
119F ARG* 1.3 79.2 - - - +
121F ALA* 1.3 61.2 + - - +
123F ILE* 4.1 3.6 - - - +
124F ALA* 3.6 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F HIS* 3.2 15.6 + - + +
120F ALA* 1.3 78.2 - - - +
122F LEU* 1.3 61.9 + - - +
123F ILE 3.2 0.7 - - - -
124F ALA* 5.1 2.0 - - - -
125F ARG* 3.0 43.4 + - - +
188F LEU* 5.4 0.5 - - - +
192F LEU* 4.2 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F PHE* 4.4 9.0 - - + +
115F ILE* 4.1 34.1 - - + +
118F HIS* 2.9 19.3 + - + +
119F ARG 3.7 0.4 + - - +
121F ALA* 1.3 74.7 - - - +
123F ILE* 1.3 64.7 + - - +
125F ARG 4.3 0.4 - - - -
126F VAL* 3.2 42.2 - - + +
159F MET* 3.3 12.4 - - + +
163F PHE* 3.7 27.8 - - + -
177F LEU* 5.6 0.4 - - + -
181F LEU* 4.0 17.7 - - + -
188F LEU* 4.3 9.9 - - + -
189F VAL* 6.1 0.9 - - + -
192F LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TRP* 6.3 0.2 - - + -
134C ASP* 3.4 30.7 - - - +
119F ARG* 3.3 38.2 + - - +
120F ALA 4.2 4.0 - - - +
121F ALA 3.2 0.6 - - - -
122F LEU* 1.3 80.9 - - - +
124F ALA* 1.3 64.1 + - + +
125F ARG 3.4 0.5 + - - -
126F VAL 4.2 4.2 + - - +
156F PRO* 3.3 42.6 - - + +
159F MET* 3.8 10.8 - - + +
160F ARG* 3.7 36.6 - - + +
163F PHE* 3.8 17.3 - - + -
144G GLU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TRP* 4.9 7.4 - - + +
120F ALA 3.6 14.4 + - - +
121F ALA* 3.5 2.5 + - - -
123F ILE* 1.3 80.9 - - + +
125F ARG* 1.3 68.9 + - + +
126F VAL 3.8 1.6 - - - +
127F THR* 5.3 1.6 - - - +
156F PRO* 4.4 9.6 - - - +
143G ASP* 4.7 6.2 - - - +
144G GLU* 2.7 30.6 - - - +
147G GLN* 5.9 0.5 + - - -
167J PRO* 4.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F ALA* 3.0 23.5 + - - +
124F ALA* 1.3 90.2 - - + +
126F VAL* 1.3 55.7 + - - +
127F THR* 4.5 0.9 - - - -
188F LEU* 3.3 24.5 - - + +
191F ASP* 3.7 20.5 + - - +
192F LEU* 3.3 31.7 - - - +
167J PRO* 2.8 28.1 + - + +
168J ALA* 2.7 37.3 - - - +
169J TRP 2.9 31.7 + - - -
170J ASN* 4.4 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F LEU* 3.2 37.7 + - + +
123F ILE 4.2 6.4 + - - +
124F ALA 5.1 0.7 - - - +
125F ARG* 1.3 76.9 + - - +
127F THR* 1.3 65.1 + - - +
128F ASN* 3.9 9.2 - - + +
129F VAL* 3.7 24.7 - - + +
132F LEU* 5.0 3.6 - - + -
155F ASN* 3.9 15.9 + - - +
156F PRO* 5.9 0.3 - - - +
159F MET* 3.9 17.6 - - + +
181F LEU* 4.2 17.9 - - + -
185F GLN* 5.3 3.6 - - - +
188F LEU* 3.7 21.3 - - + -
168J ALA* 4.5 0.4 - - - -
----------------------------------------------------------
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