Contacts of the helix formed by residues 99 - 117 (chain H) in PDB entry 3HO5
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 99 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H ILE* 6.1 1.1 - - + -
75H GLU* 5.5 4.0 - - + -
76H LEU* 4.3 9.4 - - + +
98H MET* 1.3 78.2 - - - +
100H GLN* 1.3 65.7 + - - +
101H ARG* 3.9 0.3 + - - +
102H CYS* 3.2 17.3 + - - +
103H LYS* 3.1 20.4 + - - +
142H GLU 3.9 15.3 - - - +
143H GLY 2.9 23.6 + - - +
144H ARG* 4.2 11.1 - - + +
185H VAL* 3.9 10.2 - - - +
186H LYS 4.9 1.1 + - - -
188H GLU* 3.4 27.6 + - + +
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Residues in contact with GLN 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H GLU 5.6 1.8 + - - -
77H THR* 4.6 9.7 - - - +
98H MET 4.0 0.2 + - - -
99H THR* 1.3 73.3 - - - +
101H ARG* 1.3 61.3 + - - +
103H LYS* 3.3 30.5 - - - +
104H ASP* 3.1 57.3 + - - +
188H GLU* 3.3 17.4 + - - +
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Residues in contact with ARG 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H THR* 4.2 3.8 - - - +
100H GLN* 1.3 74.3 - - - +
102H CYS* 1.3 64.7 + - - +
104H ASP* 3.2 10.0 + - - +
105H LYS* 3.2 52.0 + - - +
169H GLY 4.4 1.2 + - - -
171H ASP* 2.9 40.4 + - - -
185H VAL* 3.9 12.3 - - + +
186H LYS* 3.6 25.9 - - - +
188H GLU* 3.0 17.9 + - - +
191H VAL* 3.5 38.7 - - + +
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Residues in contact with CYS 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H MET* 3.8 20.6 - - + -
99H THR* 3.2 20.3 + - - +
101H ARG* 1.3 77.5 - - - +
103H LYS* 1.3 62.8 + - - +
105H LYS* 4.1 1.2 - - - +
106H LEU* 3.0 27.6 + - - +
143H GLY 4.2 2.2 - - - +
144H ARG 3.9 17.5 - - - -
145H ALA 4.7 0.4 - - - -
146H VAL* 3.8 30.5 - - - -
170H PHE* 4.3 12.2 - - - -
185H VAL* 3.8 18.0 - - + +
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Residues in contact with LYS 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H THR* 3.9 31.0 - - + +
78H PRO 4.4 11.2 - - - -
79H ASN* 3.9 16.9 - - - +
98H MET* 3.7 21.9 - - + -
99H THR 3.1 18.9 + - - +
100H GLN* 3.3 33.5 - - - +
102H CYS* 1.3 76.6 - - - +
104H ASP* 1.3 55.8 + - - +
106H LEU* 3.1 1.7 + - - -
107H ASN* 2.8 58.4 + - - +
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Residues in contact with ASP 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H GLN* 3.1 42.3 + - - +
101H ARG* 3.6 9.7 - - - +
103H LYS* 1.3 79.7 - - - +
105H LYS* 1.3 69.1 + - + +
107H ASN* 3.7 6.3 + - - +
108H ALA* 3.2 24.1 + - - +
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Residues in contact with LYS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ARG* 3.2 47.6 + - - +
102H CYS 4.2 0.2 - - - +
104H ASP* 1.3 81.3 - - - +
106H LEU* 1.3 57.4 - - - +
108H ALA* 3.4 4.0 + - - +
109H LEU* 3.0 27.4 + - - +
168H ALA* 3.5 22.9 + - - +
169H GLY* 3.4 31.5 + - - +
170H PHE* 3.7 27.6 - - + -
185H VAL* 3.9 13.9 - - + -
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H ASN* 3.9 4.7 - - - +
84H ILE* 3.9 17.9 - - + -
86H PHE* 4.4 2.9 - - + -
98H MET* 3.6 31.2 - - + -
102H CYS* 3.0 20.3 + - - +
103H LYS* 3.7 2.7 - - - +
105H LYS* 1.3 74.7 - - - +
107H ASN* 1.3 60.7 + - - +
109H LEU* 3.3 4.4 + - + +
110H ALA* 3.0 24.6 + - - +
122H LEU* 3.7 23.8 - - + +
124H VAL* 4.1 15.0 - - + -
146H VAL* 3.9 27.8 - - + -
148H ILE* 4.1 11.0 - - + -
170H PHE* 3.6 12.3 - - + -
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Residues in contact with ASN 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ASN* 3.2 21.6 + - - +
81H ASN* 2.9 30.2 + - - +
84H ILE* 3.5 4.0 - - - +
103H LYS* 2.8 48.6 + - - +
104H ASP* 4.2 5.8 + - - +
106H LEU* 1.3 69.0 - - - +
108H ALA* 1.3 63.7 + - - +
110H ALA* 3.4 10.6 + - - +
111H ILE* 3.2 23.4 - - + +
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Residues in contact with ALA 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H ASP 3.2 19.7 + - - +
105H LYS* 3.5 5.4 - - + +
106H LEU 3.3 0.2 - - - -
107H ASN* 1.3 74.9 - - - +
109H LEU* 1.3 62.9 + - - +
111H ILE* 3.5 17.1 + - + +
112H SER* 3.4 19.1 + - - -
168H ALA* 4.2 19.3 - - + +
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Residues in contact with LEU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H LYS 3.0 13.3 + - - +
106H LEU* 3.4 9.4 - - + +
108H ALA* 1.3 75.6 - - - +
110H ALA* 1.3 63.5 + - - +
112H SER* 3.0 18.2 + - - +
113H VAL* 3.0 24.9 + - + +
122H LEU* 3.8 31.4 - - + -
148H ILE* 3.8 16.6 - - + -
161H LEU 4.3 3.4 - - - +
164H LEU* 3.4 43.1 - - + +
165H ALA* 3.6 7.0 - - + +
168H ALA* 3.9 7.3 - - + +
170H PHE* 3.7 23.1 - - + -
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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H ASN* 4.2 6.5 - - - +
83H ASP* 4.1 14.4 - - + +
84H ILE* 3.7 32.5 - - + -
106H LEU 3.0 9.2 + - - +
107H ASN 3.4 11.2 - - - +
108H ALA 3.3 0.2 - - - -
109H LEU* 1.3 75.4 - - - +
111H ILE* 1.3 62.7 + - + +
113H VAL* 3.5 2.3 + - - +
114H MET* 3.2 30.0 + - - +
122H LEU* 4.1 13.8 + - + +
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Residues in contact with ILE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ASP* 6.1 1.3 - - - +
107H ASN* 3.2 20.2 - - + +
108H ALA* 3.7 15.5 - - - +
109H LEU 3.2 0.6 - - - -
110H ALA* 1.3 78.9 - - + +
112H SER* 1.3 61.0 + - - +
114H MET* 3.6 8.7 + - - +
115H ASN* 3.2 22.0 + - + +
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Residues in contact with SER 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H ALA 3.4 6.2 + - - -
109H LEU* 3.0 29.3 + - - +
111H ILE* 1.3 76.0 - - - +
113H VAL* 1.3 59.0 + - - +
115H ASN* 3.3 9.4 + - - +
116H GLN* 2.8 30.7 + - - +
164H LEU* 3.7 28.7 + - - +
168H ALA* 5.3 0.5 - - - +
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Residues in contact with VAL 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H LEU* 3.0 40.8 + - + +
110H ALA 3.9 3.8 - - - +
111H ILE 3.4 0.2 - - - -
112H SER* 1.3 74.2 - - - +
114H MET* 1.3 58.8 + - - +
116H GLN* 3.8 0.5 - - - +
117H TRP* 3.0 48.3 + - + +
120H VAL* 4.1 6.5 - - + +
121H LYS 3.9 8.3 - - - +
122H LEU* 3.9 28.9 - - + +
150H THR* 4.7 4.7 - - + -
161H LEU* 3.9 18.2 - - + -
164H LEU* 4.0 13.5 - - + -
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Residues in contact with MET 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H ASP* 3.6 43.1 - - - +
110H ALA 3.2 18.4 + - - +
111H ILE* 3.8 7.2 - - - +
112H SER 3.4 0.2 - - - -
113H VAL* 1.3 75.6 - - - +
115H ASN* 1.3 58.3 + - - +
117H TRP 3.4 13.6 - - - +
118H PRO* 3.8 8.3 - - - +
119H GLY 5.0 1.5 + - - +
120H VAL 3.4 20.9 - - - +
121H LYS* 4.1 21.5 - - + -
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Residues in contact with ASN 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H ILE* 3.2 17.7 + - + +
112H SER* 3.5 9.6 + - - +
113H VAL 3.1 0.6 - - - -
114H MET* 1.3 78.1 - - - +
116H GLN* 1.3 69.3 + - - +
118H PRO* 4.6 6.6 - - - +
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Residues in contact with GLN 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU* 4.6 9.9 - - - +
112H SER 2.8 20.2 + - - +
113H VAL 3.3 2.7 + - - +
115H ASN* 1.3 80.2 + - - +
117H TRP* 1.3 92.8 + - + +
118H PRO* 3.8 5.2 - - - +
160H MET* 3.9 30.6 - - + +
164H LEU* 3.8 24.8 - - + +
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Residues in contact with TRP 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H VAL* 3.0 41.5 + - + +
114H MET 3.4 7.1 - - - +
116H GLN* 1.3 94.1 - - + +
118H PRO* 1.3 69.3 - - + +
120H VAL* 3.3 32.6 + - + +
150H THR* 3.9 21.8 - - + -
157H LYS* 3.5 61.9 - - + +
160H MET* 3.6 26.0 - - + -
161H LEU* 3.8 15.7 - - + -
164H LEU* 3.9 16.8 - - + -
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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
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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