Contacts of the helix formed by residues 84 - 107 (chain A) in PDB entry 2HR9
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 THR 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 1.3 81.6 - - - +
85A LYS* 1.3 70.6 + - - +
86A GLU* 4.4 3.3 - - - +
87A ALA* 2.7 32.1 + - - +
88A TYR* 3.0 27.7 + - - +
129A PHE* 4.8 6.9 - - - -
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 1.3 80.7 - - - +
86A GLU* 1.3 69.3 + - + +
88A TYR* 3.3 14.2 + - - +
89A LYS* 3.4 28.7 + - - +
126A LEU* 4.4 13.7 - - + +
129A PHE* 5.0 29.0 - - + -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 4.4 3.0 + - - +
85A LYS* 1.3 78.8 - - - +
87A ALA* 1.3 66.7 + - - +
89A LYS* 3.1 37.9 + - + +
90A LYS* 3.4 6.4 + - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.7 22.8 - - + -
84A THR* 2.7 25.5 + - - +
85A LYS 3.3 0.4 - - - -
86A GLU* 1.3 79.7 - - - +
88A TYR* 1.3 52.2 + - - +
90A LYS* 3.2 7.3 + - - +
91A TYR* 2.7 36.0 + - - +
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 4.3 5.1 - + - -
84A THR 3.0 18.3 + - - +
85A LYS 3.5 6.5 - - - +
87A ALA* 1.3 76.2 - - - +
89A LYS* 1.3 53.9 + - - +
91A TYR* 3.3 31.5 - + - +
92A ILE* 2.7 38.9 + - + +
95A TYR* 5.6 6.3 - + - -
122A ILE* 3.1 40.6 - - + +
125A ILE* 3.5 16.0 - - + +
126A LEU* 3.4 18.6 - - + -
129A PHE* 6.1 0.2 - + - -
134A PHE* 3.1 38.6 - + - -
146A VAL* 4.2 9.7 - - + +
148A LEU* 3.3 26.8 - - + +
163A PHE* 5.4 2.9 - - - -
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 3.4 24.8 + - - +
86A GLU* 3.1 29.3 + - + +
88A TYR* 1.3 78.7 - - - +
90A LYS* 1.3 59.0 + - - +
92A ILE* 2.7 27.7 - - - +
93A LYS* 3.5 8.1 + - - +
126A LEU* 4.0 23.4 - - + +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU 3.4 5.7 + - - +
87A ALA* 3.2 9.0 + - - +
89A LYS* 1.3 78.7 + - - +
91A TYR* 1.3 60.5 + - - +
93A LYS* 3.3 45.8 + - - +
94A ASP* 3.0 29.6 + - + +
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 5.5 0.2 - - - +
83A PHE* 3.0 45.6 - + + -
87A ALA 2.7 18.9 + - - +
88A TYR* 3.3 30.1 - + - +
90A LYS* 1.3 75.8 - - - +
92A ILE* 1.3 60.3 + - - +
94A ASP* 3.2 8.9 + - + +
95A TYR* 2.8 39.4 + + + +
136A ILE* 4.9 7.8 - - - +
141A ASN 4.5 1.6 + - - -
142A PRO* 3.3 36.6 + - + +
144A GLY 4.5 7.3 + - - -
145A MET 4.5 2.1 + - - -
146A VAL* 3.1 35.3 - - + +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 2.7 20.0 + - + +
89A LYS* 2.7 33.0 - - - +
91A TYR* 1.3 72.4 - - - +
93A LYS* 1.3 58.5 + - + +
95A TYR* 3.0 46.2 - - + +
96A MET* 2.6 58.8 + - + +
118A ALA* 4.2 16.2 - - + +
119A ALA* 5.2 1.6 - - - -
122A ILE* 3.9 37.9 - - + -
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS 3.5 9.6 + - - +
90A LYS* 3.3 44.3 - - - +
91A TYR 3.3 0.4 - - - -
92A ILE* 1.3 81.8 - - + +
94A ASP* 1.3 57.7 + - - +
96A MET* 3.5 24.5 - - + +
97A LYS* 3.0 34.0 + - + +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 3.0 20.2 + - + +
91A TYR* 3.6 10.9 - - + +
93A LYS* 1.3 77.6 - - - +
95A TYR* 1.3 60.8 + - - +
97A LYS* 2.7 34.0 + - - +
98A SER* 3.3 11.1 + - - -
142A PRO 4.7 4.0 - - - +
143A ASP* 4.0 26.4 - - - +
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 5.2 0.3 - - - +
88A TYR* 5.6 6.1 - + - -
91A TYR* 2.8 26.3 + + + +
92A ILE* 3.0 47.7 - - + +
94A ASP* 1.3 72.4 + - - +
96A MET* 1.3 69.3 + - - +
97A LYS 3.2 0.2 - - - -
98A SER* 3.2 15.5 + - - -
99A ILE* 3.3 31.1 + - + +
114A PHE* 4.1 9.2 - + - -
118A ALA* 4.9 4.5 + - - +
122A ILE* 5.3 4.3 - - + +
142A PRO 5.6 0.2 - - - +
143A ASP 4.7 2.0 - - - -
144A GLY 3.4 22.4 - - - +
145A MET* 4.3 8.1 - - - -
146A VAL* 5.3 8.7 - - + -
163A PHE* 2.7 59.7 - + - -
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 2.6 47.9 + - + +
93A LYS* 3.5 31.6 - - + +
95A TYR* 1.3 77.5 - - - +
97A LYS* 1.3 56.6 + - + +
99A ILE 3.4 0.2 + - - -
100A LYS* 2.7 36.6 + - + +
114A PHE* 3.3 25.0 - - + -
115A MET* 4.7 28.0 - - - +
118A ALA* 4.3 13.0 - - + -
119A ALA* 5.4 4.5 - - + -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS* 3.0 20.1 + - + +
94A ASP* 2.7 39.3 + - - +
96A MET* 1.3 82.2 - - + +
98A SER* 1.3 64.6 + - - +
100A LYS* 3.8 11.2 - - + +
101A GLY* 2.8 28.4 + - - -
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.1 14.3 - - - +
94A ASP* 3.5 10.1 + - - -
95A TYR 3.2 10.2 + - - -
97A LYS* 1.3 91.1 - - - +
99A ILE* 1.3 60.3 + - - +
102A LYS* 3.3 28.6 + - - +
143A ASP* 2.9 37.6 + - - -
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.0 5.1 - - + +
8A ILE* 3.7 20.6 - - + -
95A TYR* 3.3 47.4 + - + +
96A MET 3.9 0.2 - - - +
98A SER* 1.3 76.6 - - - +
100A LYS* 1.3 55.4 + - - +
102A LYS* 3.3 4.3 + - - +
103A LEU* 2.6 41.2 + - + +
114A PHE* 3.7 19.7 - - + -
145A MET* 4.6 4.3 - - + -
163A PHE* 4.7 1.6 - - + -
165A ASP* 2.8 41.7 - - + +
166A GLY* 3.2 20.6 - - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A MET* 2.7 25.3 + - + +
97A LYS* 3.8 10.5 - - + +
99A ILE* 1.3 73.1 - - - +
101A GLY* 1.3 52.9 + - - +
103A LEU* 3.2 7.3 + - - +
104A GLU* 2.7 70.0 + - - +
111A VAL* 3.5 20.3 - - + +
114A PHE* 4.2 11.4 - - + -
115A MET* 4.6 31.2 - - + +
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LYS 2.8 20.9 + - - -
98A SER 4.4 0.2 - - - -
100A LYS* 1.3 74.0 - - - +
102A LYS* 1.3 61.7 + - - +
104A GLU* 3.1 31.6 + - - +
105A GLU* 3.3 8.1 + - - +
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.8 42.2 + - + -
8A ILE* 4.3 17.3 + - + +
10A HIS* 5.5 7.0 - - - -
98A SER* 3.3 26.4 + - - +
99A ILE 3.3 3.3 + - - +
101A GLY* 1.3 74.6 - - - +
103A LEU* 1.3 59.0 + - - +
105A GLU* 2.7 46.4 + - + +
106A GLN* 3.2 17.9 + - - +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.7 1.9 - - + +
99A ILE* 2.6 24.6 + - + +
100A LYS* 3.5 4.5 - - - +
102A LYS* 1.3 70.2 - - - +
104A GLU* 1.3 60.5 + - - +
106A GLN* 2.8 13.3 + - - +
107A ARG* 2.5 55.6 + - + +
108A PRO 3.0 3.5 - - - -
110A ARG* 3.3 44.2 - - + +
111A VAL* 3.4 9.4 - - + +
114A PHE* 4.7 3.6 - - + -
165A ASP* 3.9 33.7 - - + +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 2.7 46.3 + - - +
101A GLY* 3.1 27.2 + - - +
103A LEU* 1.3 72.8 - - - +
105A GLU* 1.3 55.2 + - - +
108A PRO* 3.0 30.8 - - + +
111A VAL* 3.4 25.0 - - + +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLY 3.3 4.4 + - - +
102A LYS* 2.7 46.3 - - - +
103A LEU 3.0 1.0 - - - -
104A GLU* 1.3 79.8 - - - +
106A GLN* 1.3 74.8 + - + +
108A PRO* 4.3 1.5 - - - +
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.6 36.6 - - - +
102A LYS* 3.3 20.4 + - - +
103A LEU* 2.8 10.4 + - + +
105A GLU* 1.3 94.1 - - + +
107A ARG* 1.3 76.1 + - + +
108A PRO* 3.3 8.7 - - - +
168A GLU* 4.6 12.5 + - - +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 2.5 31.9 + - + +
106A GLN* 1.3 86.7 + - + +
108A PRO* 1.3 52.6 - - - +
109A GLU* 2.9 34.8 + - + +
110A ARG* 2.6 53.4 + - + +
111A VAL 3.6 0.2 + - - -
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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) + - + + + + + -
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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