Contacts of the helix formed by residues 120 - 132 (chain G) in PDB entry 1HQ3
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 MET 120 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G THR* 4.6 0.3 - - - +
116G ARG* 3.7 26.9 - - - +
118G THR* 3.8 11.4 - - + +
119G ILE* 1.3 79.7 - - - +
121G PRO* 1.3 76.2 - - + +
122G LYS* 3.2 22.2 - - + +
123G ASP* 2.9 26.5 + - - +
124G ILE* 3.5 6.5 + - - +
608G CL 3.8 20.4 - - + -
47H SER* 4.1 12.1 - - - +
49H LEU* 5.9 4.5 - - + -
50H ILE* 4.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G MET* 1.3 89.0 - - + +
122G LYS* 1.3 56.7 + - - +
124G ILE* 3.1 7.7 + - + +
125G GLN* 2.8 40.7 + - - +
608G CL 3.7 14.6 - - + -
47H SER* 4.4 2.9 - - - +
49H LEU* 3.6 45.8 - - + +
50H ILE* 4.2 6.7 - - + +
53H GLU* 4.1 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C HIS* 3.9 22.6 + - + +
115C LYS* 4.4 23.6 - - - +
116G ARG* 3.4 28.8 - - - +
120G MET* 3.8 24.6 - - + +
121G PRO* 1.3 79.5 - - - +
123G ASP* 1.3 62.3 + - - +
125G GLN* 3.6 15.2 + - - +
126G LEU* 2.9 28.9 + - - +
608G CL 3.4 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C HIS* 2.9 16.3 + - - -
107G THR* 3.5 22.9 - - + +
110G CYS* 3.9 8.3 - - + +
111G ALA* 3.2 21.9 + - - +
116G ARG* 2.9 38.5 + - - -
119G ILE* 3.3 0.5 - - - -
120G MET* 2.9 30.0 + - - +
122G LYS* 1.3 74.1 - - - +
124G ILE* 1.3 60.6 + - - +
126G LEU* 3.3 2.4 + - - +
127G ALA* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LEU* 4.2 16.8 - - + -
104G PHE* 4.5 11.2 - - + -
107G THR* 3.5 29.6 - - + +
120G MET 4.1 6.1 - - - +
121G PRO* 3.1 7.5 + - + +
123G ASP* 1.3 76.6 - - - +
125G GLN* 1.3 59.6 + - - +
127G ALA* 3.3 3.1 + - - +
128G ARG* 2.9 47.9 + - - +
134G ARG* 4.8 0.2 - - - +
50H ILE* 4.5 14.4 - - + -
53H GLU* 3.9 27.6 - - + +
54H THR* 4.1 20.2 - - - +
57H VAL* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G PRO* 2.8 22.3 + - - +
122G LYS* 3.6 17.4 + - - +
124G ILE* 1.3 76.3 - - - +
126G LEU* 1.3 60.8 + - - +
129G ARG* 3.0 28.6 + - - +
134G ARG* 2.7 31.9 - - - +
53H GLU* 3.3 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 3.9 31.4 - - + +
110C CYS* 4.5 12.8 - - - -
113C HIS* 3.5 38.6 - - + +
126C LEU* 4.8 2.5 - - + -
110G CYS* 3.5 21.8 - - - -
122G LYS 2.9 17.6 + - - +
123G ASP 3.7 3.8 - - - +
125G GLN* 1.3 72.7 - - - +
127G ALA* 1.3 67.7 + - - +
129G ARG* 3.1 7.5 + - + +
130G ILE* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ILE* 3.9 9.8 - - - +
103G LEU* 4.2 7.2 - - + -
106G ASP* 3.8 30.5 - - + -
107G THR* 4.1 12.6 - - - +
110G CYS* 4.0 7.8 - - - -
123G ASP 3.0 17.1 + - - +
124G ILE 3.6 4.5 - - - +
126G LEU* 1.3 77.7 - - - +
128G ARG* 1.3 56.8 + - - +
130G ILE* 3.3 1.6 + - - -
131G ARG* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G TYR* 3.2 8.3 + - - -
103G LEU* 3.9 16.6 - - + -
124G ILE* 2.9 32.0 + - - +
125G GLN 3.9 4.0 - - - +
127G ALA* 1.3 75.0 - - - +
129G ARG* 1.3 66.2 + - - +
131G ARG* 3.1 5.7 + - - +
132G GLY 3.0 4.2 + - - -
133G GLU* 2.6 88.4 + - + +
134G ARG* 2.5 49.5 + - - +
57H VAL* 4.0 21.0 + - - +
60H VAL* 4.8 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ASP* 5.2 2.0 - - - +
109C LEU* 3.6 42.2 - - + +
110E ASN* 6.0 0.2 - - - +
112E GLN* 4.2 16.8 + - - +
125G GLN* 3.0 16.4 + - + +
126G LEU* 3.3 13.5 - - + +
128G ARG* 1.3 75.8 - - - +
130G ILE* 1.3 66.5 + - + +
132G GLY 3.0 11.3 + - - -
134G ARG* 4.1 14.5 - - + +
135G ALA* 3.2 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ASP* 3.9 36.2 - - + +
109C LEU* 5.1 2.7 - - + -
110C CYS* 3.5 32.8 - - - -
127C ALA* 3.9 11.2 - - - +
130C ILE* 3.7 23.6 - - + -
131C ARG* 3.7 33.8 - - + +
126G LEU* 3.0 31.2 + - + +
127G ALA 3.9 3.1 - - - +
129G ARG* 1.3 78.9 - - + +
131G ARG* 1.3 59.9 + - - +
132G GLY 3.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ILE* 4.0 18.2 - - + +
131C ARG* 5.8 0.9 - - - +
99G TYR* 3.7 20.2 + - - -
102G GLY* 3.2 30.3 + - - -
103G LEU* 3.9 23.3 - - - +
106G ASP* 2.8 27.0 + - - +
127G ALA 3.0 21.1 + - - +
128G ARG 3.5 5.6 - - - +
129G ARG 3.1 0.4 - - - -
130G ILE* 1.3 76.5 - - - +
132G GLY* 1.3 59.2 + - - +
133G GLU* 2.8 44.5 + - + +
95H ARG* 5.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G ARG 3.0 0.2 + - - -
129G ARG 3.0 7.3 + - - -
130G ILE 3.2 1.4 - - - -
131G ARG* 1.3 80.8 - - - +
133G GLU* 1.3 59.6 + - - +
134G ARG 3.3 5.7 + - - -
135G ALA* 3.6 23.5 + - - +
----------------------------------------------------------
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