Contacts of the helix formed by residues 103 - 117 (chain A) in PDB entry 1HQC
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLY 4.8 0.4 + - - -
74A ILE 3.2 21.6 + - - -
75A GLU* 3.6 14.3 + - - -
76A LYS* 5.6 0.4 - - - -
102A LEU* 1.3 74.2 - - - +
104A ARG* 1.3 68.0 + - - +
105A GLN* 3.9 12.8 - - - -
106A ALA* 2.8 22.1 + - - +
107A GLU* 2.7 25.1 + - - +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU 3.5 4.2 + - - -
103A SER* 1.3 71.9 - - - +
105A GLN* 1.3 62.5 + - + +
107A GLU* 3.6 11.1 - - - +
108A GLU* 3.3 38.3 + - - +
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Residues in contact with GLN 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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75A GLU 5.0 3.8 - - - +
76A LYS* 5.1 0.3 - - - +
77A PRO* 3.9 29.6 - - + +
103A SER* 2.8 16.7 + - - -
104A ARG* 1.3 71.8 - - + +
106A ALA* 1.3 73.9 + - - +
107A GLU 3.0 1.6 - - - -
108A GLU* 2.8 25.4 + - - +
109A HIS* 2.9 22.2 + - + +
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Residues in contact with ALA 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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74A ILE* 3.4 31.0 - - + -
77A PRO* 4.6 12.1 - - + -
80A LEU* 3.4 13.8 - - - +
102A LEU* 4.7 3.8 - - + -
103A SER* 2.8 32.5 + - - +
105A GLN* 1.3 78.8 - - + +
107A GLU* 1.3 64.2 + - - +
109A HIS* 3.2 9.9 + - - +
110A LEU* 3.1 13.9 + - - +
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Residues in contact with GLU 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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102A LEU* 4.3 29.8 - - + +
103A SER 2.7 18.5 + - - +
104A ARG* 3.6 11.3 - - - +
106A ALA* 1.3 69.1 - - - +
108A GLU* 1.3 55.2 + - - +
109A HIS 2.7 5.4 + - - -
110A LEU* 2.5 28.4 + - - +
111A TYR* 2.6 48.5 + - + -
153A ALA* 4.6 9.7 + - - +
155A LEU* 3.6 25.8 + - + +
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Residues in contact with GLU 108 (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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104A ARG* 3.3 35.6 + - - +
105A GLN* 2.8 19.6 + - - +
107A GLU* 1.3 75.2 - - + +
109A HIS* 1.3 60.5 + - + +
111A TYR* 3.8 20.4 - - + +
112A PRO* 3.0 23.2 - - - +
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Residues in contact with HIS 109 (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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77A PRO* 3.1 41.2 - - + +
80A LEU* 4.3 7.9 - - + -
105A GLN* 2.9 24.8 + - - +
106A ALA* 3.4 7.4 - - - +
107A GLU 2.7 5.5 + - - -
108A GLU* 1.3 76.3 - - + +
110A LEU* 1.3 63.9 + - - +
111A TYR 3.2 0.4 - - - -
112A PRO* 3.2 13.4 - - - +
113A ALA* 3.6 13.3 + - - +
119A MET* 4.2 25.4 - - - +
120A ASP* 3.9 28.9 + - + +
121A ILE* 5.0 5.8 - - + -
122A VAL* 5.7 8.1 - - + +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.7 28.0 - - + +
84A LEU* 4.4 10.8 - - + -
94A LEU* 4.8 0.2 - - + -
96A ILE* 4.6 4.9 - - + -
99A ILE* 4.0 13.2 - - + -
102A LEU* 4.1 11.2 - - + -
106A ALA 3.1 10.0 + - - +
107A GLU* 2.5 19.8 + - - +
109A HIS* 1.3 70.2 - - - +
111A TYR* 1.3 71.0 + - + +
113A ALA* 3.4 3.5 + - + +
114A MET* 2.9 44.1 + - + +
139A PHE* 5.6 0.4 - - + -
141A LEU* 3.4 33.4 - - + -
155A LEU* 3.9 16.8 - - + -
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Residues in contact with TYR 111 (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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107A GLU* 2.6 59.4 + - + -
108A GLU* 3.8 16.2 - - + +
110A LEU* 1.3 83.2 - - + +
112A PRO* 1.3 72.1 - - + +
114A MET* 3.0 2.8 + - - +
115A GLU* 2.9 20.9 + - - +
153A ALA* 4.8 0.7 - - - +
154A PRO* 3.7 34.5 - - + +
155A LEU* 4.4 13.2 - - + -
158A ARG* 3.6 45.2 - - - +
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Residues in contact with PRO 112 (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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108A GLU 3.0 19.1 - - - +
109A HIS* 3.2 12.3 - - - +
111A TYR* 1.3 94.0 - - + +
113A ALA* 1.3 56.4 + - - +
115A GLU* 3.1 5.8 + - + +
116A ASP* 2.7 35.7 + - + +
117A PHE 3.3 3.3 + - - -
118A VAL 3.1 20.8 - - - +
119A MET* 4.6 4.5 - - - -
120A ASP 5.5 1.8 - - - +
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Residues in contact with ALA 113 (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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84A LEU* 3.8 20.0 - - + -
109A HIS 3.6 9.7 + - - +
110A LEU* 3.4 7.6 + - + +
112A PRO* 1.3 78.5 - - - +
114A MET* 1.3 62.8 + - - +
117A PHE* 3.2 21.0 + - - -
118A VAL 3.7 6.2 + - - +
119A MET* 4.5 2.5 - - + -
136A LEU* 3.3 33.0 - - + -
139A PHE* 3.5 16.8 - - + -
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Residues in contact with MET 114 (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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40A HIS* 3.0 63.8 + - + +
110A LEU* 2.9 55.4 + - + +
111A TYR 3.5 2.9 - - - +
113A ALA* 1.3 76.7 - - - +
115A GLU* 1.3 63.0 + - - +
117A PHE* 4.0 5.6 - - - -
139A PHE* 4.6 2.5 - - + -
141A LEU* 3.3 35.9 - - + -
155A LEU* 4.3 13.2 - - - -
158A ARG* 4.0 20.6 - - + +
159A PHE* 3.9 10.5 - - + -
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Residues in contact with GLU 115 (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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111A TYR 2.9 15.2 + - - +
112A PRO* 3.7 4.4 - - + +
114A MET* 1.3 80.6 - - - +
116A ASP* 1.3 83.6 + - - +
117A PHE* 3.7 8.8 - - - -
158A ARG* 3.2 40.1 + - + +
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Residues in contact with ASP 116 (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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112A PRO* 2.7 14.5 + - + +
115A GLU* 1.3 103.7 - - - +
117A PHE* 1.3 74.2 + - - +
118A VAL* 3.4 16.5 - - + +
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Residues in contact with PHE 117 (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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40A HIS* 3.9 13.0 - + - -
112A PRO 3.3 0.4 + - - -
113A ALA* 3.2 15.9 + - - +
114A MET 4.0 11.4 - - - -
115A GLU 4.1 5.6 - - - -
116A ASP* 1.3 84.8 - - - +
118A VAL* 1.3 67.1 + - - +
135A GLU* 3.9 0.9 - - - +
136A LEU* 3.0 37.0 + - - +
137A PRO 2.9 20.0 - - - +
138A ARG* 3.3 31.4 - - + -
139A PHE* 3.2 53.8 - + - -
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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
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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