Contacts of the helix formed by residues 108 - 121 (chain F) in PDB entry 1H48
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 108 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 3.8 20.1 - - + +
24F ARG 4.8 2.5 - - - -
25F ILE* 3.7 37.7 - - + +
26F PRO* 4.4 14.7 - - + +
104F LYS 3.4 24.9 + - - -
105F MET 2.9 7.4 + - - +
107F PRO* 1.3 90.0 + - + +
109F ILE* 1.3 64.9 + - - +
110F PRO* 3.4 2.2 - - - -
111F GLN* 3.1 10.5 + - - +
112F MET* 3.1 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E GLY* 6.4 0.4 - - - -
56E ASP* 4.9 0.4 - - - +
98F ILE* 5.0 0.4 - - + -
105F MET* 3.6 18.4 - - + +
106F LEU* 3.3 28.2 + - + +
108F HIS* 1.3 76.6 - - - +
110F PRO* 1.3 72.7 - - + +
112F MET* 3.0 15.4 + - + +
113F ARG* 2.9 36.5 + - - +
129F VAL* 3.7 47.8 - - + +
130F LYS* 4.1 19.3 - - - -
131F ALA* 4.2 7.9 - - + +
901F C5P 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU 3.7 6.1 - - - +
107F PRO* 3.7 13.0 - - + +
108F HIS 3.5 3.6 - - - -
109F ILE* 1.3 96.8 - - + +
111F GLN* 1.3 60.2 + - - +
113F ARG* 3.3 12.1 + - + +
114F VAL* 3.0 28.3 + - + +
124F MET* 4.4 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 3.8 22.4 - - + -
107F PRO 5.3 0.2 + - - -
108F HIS* 3.1 12.0 + - - +
110F PRO* 1.3 76.4 - - - +
112F MET* 1.3 66.5 + - - +
114F VAL* 3.2 21.2 + - - +
115F PHE* 3.0 55.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ILE* 3.6 41.5 - - + +
21F GLY* 3.6 20.9 - - - +
23F VAL* 3.7 6.0 - - + +
25F ILE* 4.0 8.7 - - + -
40F ALA* 5.6 0.7 - - - -
98F ILE* 4.0 12.8 - - + -
105F MET* 4.4 9.0 - - - +
108F HIS* 3.1 36.8 + - + +
109F ILE* 3.0 12.0 + - + +
111F GLN* 1.3 75.5 - - - +
113F ARG* 1.3 57.5 + - - +
115F PHE* 3.2 3.1 + - - +
116F ILE* 2.8 40.9 + - + +
129F VAL* 4.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ALA* 4.7 15.7 + - - +
109F ILE* 2.9 31.9 + - - +
110F PRO* 3.6 10.8 - - - +
112F MET* 1.3 73.1 - - - +
114F VAL* 1.3 66.5 + - - +
116F ILE* 4.2 0.2 - - - +
117F ALA* 3.0 28.4 + - - +
124F MET* 2.9 61.0 + - + +
125F ASP* 4.1 7.7 + - - +
127F VAL* 2.9 34.4 + - + +
128F ASN* 4.8 3.1 + - - +
129F VAL* 4.2 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F PRO 3.0 20.9 + - - +
111F GLN* 3.2 29.8 + - - +
113F ARG* 1.3 76.5 - - - +
115F PHE* 1.3 58.6 + - + +
117F ALA* 4.0 2.0 - - - +
118F GLU* 3.0 51.1 + - - +
124F MET* 4.1 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F GLY 3.5 21.3 - - - +
22F GLY* 3.2 28.0 - - - -
23F VAL* 3.9 11.2 - - + -
41F LEU* 6.3 0.4 - - + -
74F ARG* 3.3 39.9 - - + +
111F GLN* 3.0 40.6 + - + -
112F MET 3.4 7.2 - - - +
114F VAL* 1.3 75.5 - - + +
116F ILE* 1.3 59.9 + - + +
118F GLU* 3.3 11.2 + - - +
119F ASP* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F GLY* 4.8 4.9 - - - +
40F ALA* 6.3 1.1 - - + -
41F LEU* 3.7 31.2 - - + -
44F LEU* 3.8 24.0 - - + -
77F LEU* 4.9 0.9 - - + -
94F VAL* 4.4 2.0 - - + -
96F VAL* 5.1 5.4 - - + -
112F MET* 2.8 29.8 + - + +
113F ARG 4.2 0.2 - - - +
115F PHE* 1.3 72.3 - - + +
117F ALA* 1.3 57.9 + - - +
119F ASP* 3.1 7.5 + - - +
120F LEU* 2.9 41.2 + - + +
127F VAL* 3.7 28.0 - - + -
129F VAL* 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ARG 3.0 19.4 + - - +
114F VAL 4.0 2.7 - - - +
116F ILE* 1.3 76.4 - - - +
118F GLU* 1.3 58.4 + - - +
121F GLY* 3.0 23.6 + - - -
122F CYS* 3.0 40.7 + - - +
123F HIS 3.9 3.1 - - - -
124F MET* 3.8 26.0 - - + +
127F VAL* 4.1 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ARG* 4.2 16.0 + - - +
78F ARG* 5.5 0.5 - - - -
114F VAL* 3.0 40.7 + - - +
115F PHE* 3.5 9.9 - - - +
116F ILE 3.2 0.2 - - - -
117F ALA* 1.3 76.2 - - - +
119F ASP* 1.3 62.7 + - - +
120F LEU 3.3 0.5 + - - -
121F GLY* 3.3 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU* 4.9 0.5 - - - +
74F ARG* 2.9 43.4 + - - +
77F LEU* 3.7 25.3 - - + +
78F ARG* 2.9 53.6 + - + +
81F TRP* 3.7 14.0 - - - +
115F PHE* 2.9 19.1 + - - +
116F ILE* 3.6 4.7 - - - +
118F GLU* 1.3 76.8 - - - +
120F LEU* 1.3 61.0 + - - +
121F GLY 3.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F LEU* 4.6 2.9 - - + -
48F LEU* 4.1 18.2 - - + -
77F LEU* 3.9 25.6 - - + -
81F TRP* 3.2 53.6 + - + +
85F GLN* 5.6 0.2 + - - -
91F LEU* 4.0 23.6 - - + +
94F VAL* 4.4 10.3 - - + -
116F ILE* 2.9 37.8 + - + +
119F ASP* 1.3 81.3 - - + +
121F GLY* 1.3 64.4 + - - +
122F CYS* 3.1 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ALA 3.0 6.7 + - - -
118F GLU* 3.3 10.4 + - - -
119F ASP 3.4 0.6 - - - -
120F LEU* 1.3 77.7 - - - +
122F CYS* 1.3 58.9 + - - +
----------------------------------------------------------
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