Contacts of the helix formed by residues 103 - 113 (chain A) in PDB entry 1MHQ
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 LYS 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A SER* 3.2 22.4 - - - +
100A GLU* 2.3 44.4 + - - +
101A VAL 3.1 2.4 - - - +
102A ALA* 1.3 78.7 - - - +
104A PHE* 1.3 66.2 + - - +
105A ARG* 2.7 49.3 - - + +
106A PHE* 3.3 2.6 + - - +
107A LEU* 3.1 22.5 + - - +
147A LYS* 4.9 2.9 - - - -
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Residues in contact with PHE 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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102A ALA 4.0 1.0 + - - -
103A LYS* 1.3 70.0 - - - +
105A ARG* 1.3 62.4 + - - +
107A LEU* 3.0 11.6 + - + -
108A ASN* 2.7 67.1 + - + +
111A ILE* 5.1 7.6 - - + -
147A LYS* 4.2 23.6 - - + +
150A ASP* 6.5 0.4 - - + -
151A ALA* 4.7 14.4 - - + -
154A MET* 3.7 31.4 - - + -
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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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65A TRP* 3.9 25.9 - - + -
100A GLU* 3.2 12.2 + - - +
103A LYS* 2.7 55.9 - - + +
104A PHE* 1.3 82.4 - - - +
106A PHE* 1.3 71.8 + - - +
108A ASN* 3.5 6.0 + - - +
109A GLU* 3.5 21.1 + - - +
119B LEU* 4.5 21.2 - - - +
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Residues in contact with PHE 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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64A PRO* 3.3 44.4 - - + -
65A TRP* 3.8 23.1 - + + -
67A LEU* 5.1 0.9 - - + -
68A ALA* 4.2 13.9 - - + -
71A ILE* 5.3 1.6 - - + -
86A LEU* 4.3 15.9 - - + -
100A GLU 3.6 19.7 - - - +
101A VAL* 3.4 43.7 - - + -
103A LYS 3.3 2.6 + - - +
104A PHE 3.0 0.6 - - - -
105A ARG* 1.3 81.2 - - - +
107A LEU* 1.3 68.1 + - + +
109A GLU* 2.9 15.6 + - + +
110A LEU* 3.2 39.5 + - + -
138A TRP* 4.5 2.2 - + - -
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Residues in contact with LEU 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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101A VAL 3.3 15.7 - - - +
102A ALA 3.8 5.8 - - - +
103A LYS 3.2 15.9 - - - +
104A PHE* 3.0 9.3 + - + +
106A PHE* 1.3 80.7 - - + +
108A ASN* 1.3 64.5 + - - +
110A LEU* 3.0 8.5 + - + +
111A ILE* 2.9 29.8 + - + +
135A LEU* 4.5 13.0 - - + -
138A TRP* 4.0 23.6 - - + -
147A LYS* 3.8 26.0 - - + +
148A ILE* 3.7 29.4 - - + -
151A ALA* 4.5 14.1 - - + -
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Residues in contact with ASN 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 PHE* 2.7 48.5 + - + +
105A ARG* 3.6 6.9 + - - +
107A LEU* 1.3 73.5 - - - +
109A GLU* 1.3 64.0 + - - +
111A ILE* 3.2 15.9 + - - +
112A LYS* 3.0 46.5 + - - +
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Residues in contact with GLU 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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65A TRP* 4.1 13.2 - - + -
68A ALA* 4.1 14.1 - - + -
71A ILE* 5.9 0.3 - - - +
72A GLN* 2.7 47.8 + - - +
105A ARG 3.5 13.5 + - - +
106A PHE* 2.9 10.4 + - + +
108A ASN* 1.3 81.1 + - - +
110A LEU* 1.3 63.0 + - - +
112A LYS* 3.0 42.5 + - - +
113A VAL* 4.1 2.3 + - - +
122B TRP* 3.6 27.0 - - + -
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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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68A ALA* 6.2 1.1 - - - -
71A ILE* 3.8 38.6 - - + -
83A LEU* 4.6 3.6 - - + -
86A LEU* 4.1 7.9 - - + -
106A PHE* 3.2 22.6 + - + -
107A LEU* 3.0 13.0 + - + +
109A GLU* 1.3 79.5 - - - +
111A ILE* 1.3 64.2 + - + +
113A VAL* 3.3 23.7 + - - +
114A LEU 4.3 0.2 + - - -
131A VAL* 3.9 24.6 - - + +
134A ILE* 5.2 4.0 - - + -
135A LEU* 3.9 30.5 - - + -
138A TRP* 4.1 21.8 - - + -
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Residues in contact with ILE 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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104A PHE* 5.1 9.9 - - + -
107A LEU* 2.9 23.2 + - + +
108A ASN* 3.2 17.0 + - - +
110A LEU* 1.3 73.7 - - + +
112A LYS* 1.3 59.1 + - - +
113A VAL 3.0 2.7 - - - -
114A LEU* 2.8 30.2 + - + +
115A SER* 3.5 3.5 + - - -
131A VAL* 5.4 0.2 - - - -
135A LEU* 4.7 9.0 - - + -
151A ALA* 4.1 25.8 - - + +
154A MET* 6.2 1.3 - - + -
155A LEU* 3.6 41.7 - - + -
160A ILE* 5.6 3.1 - - + -
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Residues in contact with LYS 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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72A GLN* 4.4 9.2 - - + +
108A ASN* 3.0 35.8 + - - +
109A GLU* 3.0 43.8 + - - +
110A LEU 3.3 1.0 - - - -
111A ILE* 1.3 76.3 - - - +
113A VAL* 1.3 62.1 + - - +
115A SER* 3.0 26.0 + - - +
120A GLY 4.1 2.4 - - - +
121A SER* 3.9 5.5 - - - -
112B LYS* 6.2 2.6 - - - +
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Residues in contact with VAL 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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71A ILE* 3.9 33.4 - - + +
72A GLN* 4.3 18.6 - - + -
109A GLU 4.1 0.9 + - - +
110A LEU 3.3 13.8 + - - +
111A ILE 3.0 0.2 - - - -
112A LYS* 1.3 79.9 - - - +
114A LEU* 1.3 61.7 + - + +
115A SER 3.2 0.6 + - - -
121A SER* 3.0 22.1 + - - -
123A ALA* 4.0 20.9 - - + -
127A VAL* 4.0 7.2 - - + -
128A LYS* 3.8 20.5 - - + -
131A VAL* 3.9 20.9 - - + -
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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