Contacts of the helix formed by residues 101 - 115 (chain A) in PDB entry 6AU8
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 ALA 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLU 3.4 2.5 + - - +
100A VAL* 1.3 79.7 - - - +
102A ASP* 1.3 67.8 + - - +
103A GLU* 3.2 4.3 - - + +
104A LEU* 3.1 32.3 + - + +
105A LEU* 3.1 12.8 + - - +
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Residues in contact with ASP 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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101A ALA* 1.3 72.5 - - - +
103A GLU* 1.3 62.5 + - - +
105A LEU* 3.3 8.1 + - - +
106A GLU* 3.0 41.3 + - - +
144A ARG* 4.4 21.9 + - - +
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Residues in contact with GLU 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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101A ALA* 3.2 3.9 - - + +
102A ASP* 1.3 79.3 - - - +
104A LEU* 1.3 62.6 + - + +
106A GLU* 3.3 13.8 + - - +
107A ASN* 2.9 64.9 + - - +
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Residues in contact with LEU 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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63A ARG* 3.6 30.3 - - - +
93A LEU* 4.4 10.1 - - + -
98A VAL* 3.5 31.4 - - + -
99A GLU 3.6 13.7 - - - +
101A ALA* 3.1 20.3 + - + +
103A GLU* 1.3 80.7 - - + +
105A LEU* 1.3 63.8 + - - +
107A ASN* 3.2 16.8 + - + +
108A LEU* 3.0 28.5 + - + +
132A TRP* 4.1 18.4 - - + -
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Residues in contact with LEU 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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100A VAL* 3.4 37.5 - - + -
101A ALA 3.1 7.8 + - - +
102A ASP* 3.7 9.4 - - - +
104A LEU* 1.3 79.8 - - - +
106A GLU* 1.3 56.0 + - - +
108A LEU* 3.3 5.8 + - + +
109A ALA* 2.9 29.6 + - - +
132A TRP* 4.0 21.8 - - + -
133A SER* 4.3 5.2 - - - -
142A HIS* 4.0 8.3 - - + +
144A ARG* 3.7 33.4 - - + -
145A LEU* 4.0 28.1 - - + +
148A LEU* 3.9 13.9 - - + +
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Residues in contact with GLU 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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102A ASP* 3.0 32.8 + - - +
103A GLU* 3.7 14.4 - - - +
105A LEU* 1.3 76.2 - - - +
107A ASN* 1.3 59.6 + - - +
109A ALA* 3.5 2.5 + - - +
110A LYS* 3.0 28.6 + - - +
144A ARG* 3.3 22.8 + - - +
148A LEU* 4.2 20.6 - - + -
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Residues in contact with ASN 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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63A ARG* 5.9 1.2 - - - +
67A TYR* 3.4 53.7 + - + -
103A GLU* 2.9 50.2 + - - +
104A LEU* 3.4 17.5 - - + +
106A GLU* 1.3 74.7 - - - +
108A LEU* 1.3 67.9 + - + +
110A LYS* 3.2 4.2 + - - +
111A VAL* 3.2 18.7 + - - +
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Residues in contact with LEU 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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67A TYR* 6.5 0.7 - - + -
89A VAL* 4.1 21.8 - - + -
90A LEU* 3.9 21.8 - - + -
93A LEU* 4.2 7.0 - - + -
104A LEU 3.0 19.7 + - - +
105A LEU* 3.8 9.0 - - + +
107A ASN* 1.3 80.3 - - + +
109A ALA* 1.3 61.4 + - - +
111A VAL* 3.5 3.5 + - + -
112A PHE* 3.0 18.0 + - - +
125A PHE* 3.5 35.9 - - + -
129A ALA* 4.3 9.2 - - + -
132A TRP* 3.7 36.1 - - + -
145A LEU* 4.7 10.1 - - + -
149A LEU* 5.9 0.2 - - - -
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Residues in contact with ALA 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 LEU 2.9 16.1 + - - +
106A GLU* 4.0 3.6 - - - +
108A LEU* 1.3 73.5 - - - +
110A LYS* 1.3 61.0 + - - +
112A PHE* 3.3 11.7 + - + +
113A SER* 2.9 29.1 + - - -
145A LEU* 4.6 6.0 - - + +
148A LEU* 3.6 41.7 - - + +
149A LEU* 4.8 6.5 - - + -
152A THR* 4.7 3.6 + - - +
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Residues in contact with LYS 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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67A TYR* 3.4 18.1 + - - +
71A LEU* 3.8 28.9 - - + +
106A GLU 3.0 18.3 + - - +
107A ASN 3.5 5.8 - - - +
108A LEU 3.2 0.4 - - - -
109A ALA* 1.3 78.1 - - - +
111A VAL* 1.3 62.1 + - - +
113A SER* 2.6 26.8 + - - +
114A LEU* 3.2 21.6 + - + +
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Residues in contact with VAL 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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67A TYR* 3.8 31.6 - - + -
70A ALA* 4.6 3.8 - - + -
71A LEU* 4.4 7.9 - - + -
74A PHE* 3.8 15.5 - - + -
86A SER* 3.0 34.5 - - - +
89A VAL* 6.2 1.1 - - + -
107A ASN 3.2 3.8 + - - +
108A LEU* 3.7 7.9 - - + +
110A LYS* 1.3 79.3 - - - +
112A PHE* 1.3 63.2 + - - +
114A LEU* 3.0 15.5 + - - +
115A MET* 3.2 29.4 + - + +
125A PHE* 3.8 11.9 - - + -
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Residues in contact with PHE 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 LEU 3.0 14.7 + - - +
109A ALA* 3.4 9.6 - - + +
111A VAL* 1.3 75.1 - - - +
113A SER* 1.3 62.0 + - - +
115A MET* 3.2 16.8 + - - -
122A ARG* 2.8 68.0 + - + -
125A PHE* 4.1 8.5 - + + -
126A VAL* 3.3 34.1 - - + -
149A LEU* 3.5 27.6 - - + -
152A THR* 3.8 31.6 - - + -
153A LEU* 3.9 26.2 - - + -
165A HIS* 6.0 0.7 - - - -
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Residues in contact with SER 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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109A ALA 2.9 13.1 + - - -
110A LYS* 2.6 25.9 + - - +
112A PHE* 1.3 77.5 - - - +
114A LEU* 1.3 64.8 + - - +
115A MET 3.4 3.0 - - - +
122A ARG* 4.1 1.3 - - - +
152A THR* 3.8 32.5 - - - -
156A GLU* 4.1 9.7 - - - +
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Residues in contact with LEU 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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71A LEU* 3.7 22.9 - - + +
74A PHE* 3.6 44.3 - - + -
79A GLN* 2.9 20.6 + - - -
110A LYS* 3.5 23.3 - - + +
111A VAL 3.0 7.9 + - - +
113A SER* 1.3 81.6 - - - +
115A MET* 1.3 61.0 + - - +
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Residues in contact with MET 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 PHE* 3.7 14.8 - - + -
79A GLN* 5.9 0.2 - - - -
83A ALA* 4.0 20.9 - - + +
86A SER* 3.7 18.8 - - - +
87A MET* 5.2 0.4 - - + -
111A VAL* 3.3 36.3 - - + +
112A PHE* 3.2 4.3 + - - +
113A SER 4.1 2.1 - - - +
114A LEU* 1.3 81.9 - - - +
116A ASP* 1.3 65.7 + - - +
117A PRO* 3.2 6.8 - - - +
119A SER* 4.8 2.5 - - - +
121A GLU* 4.6 2.0 - - - +
122A ARG* 3.4 48.1 + - + -
125A PHE* 3.7 35.4 - - + -
156A GLU* 5.1 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
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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