Contacts of the helix formed by residues 104 - 117 (chain A) in PDB entry 1AVZ
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 GLN 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A HIS* 4.3 7.5 - - + -
103A SER* 1.3 71.3 - - - +
105A ARG* 1.3 52.6 + - - +
107A GLN* 3.2 27.7 + - - +
108A ASP* 2.8 72.0 + - - +
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Residues in contact with ARG 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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103A SER* 3.2 8.4 - - - +
104A GLN* 1.3 78.3 - - - +
106A ARG* 1.3 58.8 - - + +
108A ASP* 3.5 7.8 + - - +
109A ILE* 2.9 52.2 + - + +
76B LEU* 4.5 7.7 - - - +
78B PRO* 5.8 5.7 - - - +
121B PHE* 3.4 53.1 - - + +
123B ASP* 4.1 8.2 + - - +
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Residues in contact with ARG 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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100A LEU* 4.1 24.2 - - + +
101A ILE* 2.9 54.1 + - - +
102A HIS 5.2 0.8 - - - -
103A SER* 2.9 29.9 + - - +
105A ARG* 1.3 76.5 - - + +
107A GLN* 1.3 66.3 + - - +
108A ASP 2.9 1.3 - - - -
109A ILE* 2.9 16.2 + - + +
110A LEU* 2.8 24.9 + - - +
183A TRP* 3.8 16.8 - - + -
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A HIS* 2.7 35.5 + - - +
103A SER 2.9 11.0 + - - +
104A GLN* 3.5 27.4 + - - +
106A ARG* 1.3 76.9 - - - +
108A ASP* 1.3 57.0 + - - +
110A LEU* 3.6 2.4 + - - +
111A ASP* 2.6 39.5 + - - +
125A GLN* 2.9 42.9 + - - +
126A ASN* 4.7 7.7 - - - +
127A TYR* 4.0 15.5 - - - +
183A TRP* 3.7 12.2 - - + -
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Residues in contact with ASP 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 GLN* 2.8 47.4 + - - +
105A ARG* 3.6 6.0 - - - +
107A GLN* 1.3 78.9 - - - +
109A ILE* 1.3 66.3 + - - +
111A ASP* 3.2 9.0 + - - +
112A LEU* 3.0 30.3 + - + +
121B PHE* 3.6 27.7 - - + -
122B PRO* 4.3 7.7 - - + +
123B ASP* 4.1 12.8 - - - +
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Residues in contact with ILE 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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105A ARG* 2.9 53.1 + - + +
106A ARG* 2.9 16.9 + - + +
108A ASP* 1.3 75.6 - - - +
110A LEU* 1.3 57.5 + - - +
112A LEU* 3.6 7.4 + - - +
113A TRP* 2.9 30.8 + - + +
76B LEU* 5.8 2.7 - - + -
121B PHE* 4.3 9.6 - - + -
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Residues in contact with LEU 110 (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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91A LEU* 4.6 11.9 - - + -
97A LEU* 3.8 38.1 - - + -
106A ARG 2.8 14.2 + - - +
107A GLN 3.6 6.3 - - - +
109A ILE* 1.3 75.8 - - - +
111A ASP* 1.3 65.4 + - - +
113A TRP* 3.2 11.3 + - + -
114A ILE* 3.0 54.0 + - + +
124A TRP* 4.6 4.0 - - + -
125A GLN* 3.5 29.4 - - - +
141A TRP* 4.5 3.1 - - + -
183A TRP* 4.2 6.5 - - + +
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Residues in contact with ASP 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 GLN* 2.6 25.1 + - - +
108A ASP* 3.2 12.7 + - - +
110A LEU* 1.3 74.9 - - - +
112A LEU* 1.3 59.7 - - + +
114A ILE* 3.8 1.9 + - - +
115A TYR* 3.1 27.9 + - - +
120A TYR 4.7 1.7 - - - +
122A PRO* 3.7 39.1 - - + +
123A ASP* 5.1 0.2 - - - -
124A TRP* 4.7 9.8 + - - +
125A GLN* 2.7 42.1 + - - +
126A ASN* 5.9 0.3 + - - -
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Residues in contact with LEU 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 ASP* 3.0 20.2 + - + +
109A ILE* 3.9 5.4 - - - +
111A ASP* 1.3 77.6 - - + +
113A TRP* 1.3 60.4 + - - +
115A TYR* 3.0 9.7 + - + +
116A HIS* 2.8 37.6 + - + +
122A PRO* 5.0 4.9 - - + -
76B LEU* 5.2 3.1 - - + -
112B LEU* 4.0 20.4 - - + -
115B TYR* 3.7 49.4 - - + +
121B PHE* 4.3 15.7 - - + -
122B PRO* 4.1 21.5 - - + -
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Residues in contact with TRP 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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90A PHE* 4.4 10.5 - + - -
91A LEU* 4.0 24.5 - - + -
94A LYS* 4.3 26.2 - - + -
109A ILE* 2.9 22.2 + - + +
110A LEU* 3.2 11.2 + - + +
112A LEU* 1.3 75.3 - - - +
114A ILE* 1.3 80.0 + - + +
116A HIS* 3.4 6.3 + - + +
117A THR* 3.1 55.2 + - + +
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Residues in contact with ILE 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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87A LEU* 3.8 33.0 - - + -
90A PHE* 5.9 0.7 - - + -
91A LEU* 4.6 2.2 - - + -
110A LEU* 3.0 33.3 + - + +
111A ASP 4.1 3.1 - - - +
113A TRP* 1.3 103.5 - - + +
115A TYR* 1.3 57.1 + - - +
117A THR* 3.8 4.5 - - - +
118A GLN* 2.6 52.7 + - + +
119A GLY 3.1 5.1 + - - -
120A TYR* 3.9 22.0 - - + -
124A TRP* 4.2 16.4 - - + +
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Residues in contact with TYR 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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74A VAL* 5.5 0.7 - - - +
76A LEU* 3.6 29.8 - - + +
111A ASP 3.1 20.3 + - - +
112A LEU* 3.0 12.7 + - + +
114A ILE* 1.3 78.4 - - - +
116A HIS* 1.3 75.2 + + - +
119A GLY* 3.3 17.3 + - - -
120A TYR 3.7 19.0 + - - +
121A PHE* 5.0 1.8 - + - -
122A PRO* 3.6 27.4 - - + -
112B LEU* 4.0 29.4 - - + +
115B TYR* 4.9 1.1 - + - -
116B HIS* 2.6 43.5 + + - -
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Residues in contact with HIS 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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74A VAL* 3.3 26.2 - - - +
112A LEU* 2.8 25.6 + - + +
113A TRP* 3.8 7.9 - - + +
115A TYR* 1.3 87.1 - + - +
117A THR* 1.3 62.9 + - + +
73B GLN* 3.6 15.1 + - + -
115B TYR* 3.0 31.9 + + - -
116B HIS* 3.6 30.9 - + - -
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Residues in contact with THR 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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74A VAL* 3.1 24.7 - - - +
77A ARG* 5.0 0.3 + - - -
113A TRP* 3.1 46.4 + - + +
114A ILE* 3.8 3.1 - - - +
116A HIS* 1.3 80.2 - - + +
118A GLN* 1.3 83.8 + - - +
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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