Contacts of the helix formed by residues 97 - 111 (chain A) in PDB entry 2HQT
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 TYR 97 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.9 19.3 - - + +
47A ASP* 3.8 22.4 + - - -
50A ASN* 3.2 15.3 - - + +
80A ILE* 4.0 20.4 - - + -
83A LEU* 4.0 27.0 - - + +
93A THR* 3.3 40.9 + - + +
94A TYR 3.6 3.8 - - - -
95A THR 3.3 0.2 - - - -
96A THR* 1.3 99.5 - - + +
98A ARG* 1.3 62.4 + - - +
100A ILE* 3.5 20.6 + - + -
101A LEU* 3.0 27.1 + - + +
47B ASP* 4.7 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 3.4 2.8 + - - +
91A LYS* 5.5 0.4 - - - +
94A TYR* 3.3 24.2 + - - +
95A THR* 3.3 44.8 + - - +
96A THR 3.7 1.2 - - - -
97A TYR* 1.3 76.3 - - - +
99A HIS* 1.3 77.7 + - + +
101A LEU* 3.3 7.1 + - - +
102A ARG* 3.0 26.2 + - - +
2002A SO4 2.4 40.0 + - - -
54B ARG* 4.0 0.8 - - - +
54C ARG* 3.4 55.4 - - + +
55C ASP* 4.3 7.8 + - - +
98D ARG* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 3.0 42.2 + - - +
51A LEU* 5.4 0.7 - - - -
53A LEU* 3.7 11.9 - - - +
54A ARG* 3.5 41.4 - - + +
98A ARG* 1.3 89.7 - - + +
100A ILE* 1.3 66.2 + - - +
102A ARG* 3.3 16.6 + - - +
103A TRP* 3.1 22.9 + - - +
54C ARG* 4.6 8.7 + - + -
99C HIS* 3.6 32.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.4 46.2 - - + +
49A LEU* 3.9 14.8 - - + -
50A ASN* 3.1 26.9 - - + +
53A LEU* 3.9 8.7 - - + +
76A ALA* 5.0 2.0 - - + -
80A ILE* 4.1 11.9 - - + -
97A TYR* 3.8 21.1 - - + +
99A HIS* 1.3 75.5 - - - +
101A LEU* 1.3 50.4 + - - +
103A TRP* 3.1 15.0 + - + +
104A ILE* 2.7 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.9 15.3 - - + -
84A VAL* 5.5 0.9 - - + -
93A THR* 4.9 1.3 - - + +
94A TYR* 3.6 63.9 - - + +
97A TYR* 3.0 20.5 + - + +
98A ARG* 3.5 5.8 - - - +
99A HIS 3.3 0.2 - - - -
100A ILE* 1.3 72.3 - - - +
102A ARG* 1.3 61.1 + - - +
104A ILE* 3.7 5.5 - - + +
105A ASP* 2.9 31.2 + - - +
119A LEU* 3.4 33.7 - - + -
121A ILE* 4.1 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 2.7 43.4 + - - +
54A ARG* 4.4 2.6 + - - +
56A ASN 3.1 16.6 + - - -
57A THR* 3.2 16.3 + - - +
98A ARG 3.0 13.1 + - - +
99A HIS* 3.3 23.8 + - - +
101A LEU* 1.3 78.0 - - - +
103A TRP* 1.3 62.7 + - - +
105A ASP* 3.4 5.8 - - - +
106A TYR* 3.1 24.3 + - - +
53C LEU 4.2 0.8 + - - -
54C ARG 3.8 17.1 + - - +
55C ASP* 3.7 28.8 - - - +
56C ASN* 3.9 5.1 - - - +
57C THR* 3.8 30.6 + - - +
99C HIS* 5.8 2.4 + - - -
102C ARG* 3.4 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.2 14.4 - - + -
53A LEU* 3.7 33.7 - - + -
57A THR 3.9 11.9 - - - -
58A PHE* 4.3 7.4 - + - -
59A ILE* 3.2 29.5 - - + +
69A ASP* 3.0 38.5 + - - -
72A VAL* 3.8 4.7 - - + -
73A PHE* 3.3 35.9 - + + -
76A ALA* 4.2 9.4 - - + -
99A HIS 3.1 13.8 + - - +
100A ILE* 3.6 10.8 - - + +
102A ARG* 1.3 83.7 - - - +
104A ILE* 1.3 71.4 + - + +
106A TYR* 3.1 6.8 + - + +
107A MET* 2.8 55.0 + - + +
57C THR* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 4.2 14.8 - - + -
76A ALA 4.2 8.5 - - - +
77A LEU* 3.9 19.1 - - + -
80A ILE* 3.9 29.8 - - + -
100A ILE* 2.7 44.2 + - + +
101A LEU* 3.7 6.7 - - + +
103A TRP* 1.3 80.2 - - + +
105A ASP* 1.3 65.7 + - - +
108A GLN* 3.0 46.1 + - - +
119A LEU* 4.5 13.5 - - + -
121A ILE* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU 2.9 18.8 + - - +
102A ARG* 3.4 8.3 - - - +
103A TRP 3.3 0.2 - - - -
104A ILE* 1.3 78.6 - - - +
106A TYR* 1.3 63.1 + - - +
108A GLN* 3.7 15.2 + - - +
109A ASN* 3.0 42.1 + - - -
121A ILE* 4.1 27.1 - - + +
55C ASP 4.4 11.2 - - - +
56C ASN* 4.8 5.9 - - - +
61C SER* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.4 39.0 - + + -
64A TYR* 5.6 2.3 - - - -
65A PRO* 4.2 8.3 - - + +
102A ARG 3.1 9.1 + - - +
103A TRP* 3.1 10.3 + - - +
105A ASP* 1.3 74.1 - - - +
107A MET* 1.3 69.0 + - - +
109A ASN* 3.3 3.3 + - - -
110A LEU* 3.0 50.3 + - + +
57C THR* 3.7 32.1 - - + +
58C PHE* 4.0 10.4 - + - -
62C THR 4.0 9.6 - - - -
63C LEU* 2.5 54.6 + - + +
64C TYR* 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 4.6 1.8 - - - -
65A PRO* 4.0 17.7 - - + -
69A ASP* 3.9 27.8 - - + +
70A VAL* 3.9 27.1 - - + +
73A PHE* 3.7 21.1 - - + -
103A TRP* 2.8 47.2 + - + +
106A TYR* 1.3 89.9 - - + +
108A GLN* 1.3 58.8 + - - +
110A LEU* 3.3 12.6 + - + +
111A LEU* 2.8 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.5 14.1 - - + -
77A LEU* 3.5 15.6 - - - +
104A ILE* 3.0 26.0 + - - +
105A ASP* 3.7 24.0 + - - +
107A MET* 1.3 77.7 - - - +
109A ASN* 1.3 62.7 + - - +
112A GLU 3.3 1.0 + - - -
113A VAL* 3.0 46.3 + - + +
118A LYS* 3.2 31.9 + - + +
119A LEU 3.2 38.3 + - - -
120A GLU 4.3 3.2 + - - -
121A ILE* 4.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 3.0 32.9 + - - +
106A TYR* 3.3 8.6 + - - +
107A MET 3.2 0.4 - - - -
108A GLN* 1.3 80.6 - - - +
110A LEU* 1.3 65.3 + - - +
112A GLU* 3.2 18.7 + - - +
118A LYS* 3.8 20.8 + - - +
63C LEU* 4.0 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 3.5 31.4 - - + -
70A VAL* 5.9 1.1 - - + -
106A TYR* 3.0 30.2 + - + +
107A MET* 3.3 22.0 + - + +
109A ASN* 1.3 75.9 - - - +
111A LEU* 1.3 69.1 + - + +
112A GLU* 3.4 14.7 + - - +
63C LEU* 3.3 23.8 - - + +
64C TYR* 4.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 4.3 27.4 - - + -
73A PHE* 3.7 30.7 - - + -
74A GLU* 6.3 0.4 - - + -
107A MET* 2.8 36.6 + - + +
110A LEU* 1.3 84.4 - - + +
112A GLU* 1.3 71.6 + - - +
113A VAL* 3.3 12.5 + - + +
----------------------------------------------------------
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