Contacts of the helix formed by residues 99 - 108 (chain A) in PDB entry 1MQ0
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 CYS 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A CYS* 4.1 0.7 - - - -
97A SER 3.8 1.8 + - - -
98A PRO* 1.3 76.0 - - - +
100A GLY* 1.3 67.4 + - - +
101A ALA* 3.5 16.8 - - - -
102A CYS* 2.9 23.5 + - - +
103A ARG* 3.1 10.6 + - - +
147A ZN 2.5 36.2 - - - -
148A BRD 4.8 6.9 - - + +
59B CYS* 3.3 35.4 - - + -
62B LEU* 4.0 2.9 - - + -
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Residues in contact with GLY 100 (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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98A PRO 3.9 1.0 + - - -
99A CYS* 1.3 72.5 - - - +
101A ALA* 1.3 56.0 + - - +
103A ARG* 3.3 17.9 + - - +
104A GLN* 2.9 29.0 + - - +
133A LEU* 4.4 8.3 - - - +
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Residues in contact with ALA 101 (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 ARG* 4.0 21.1 - - - +
99A CYS* 3.1 14.4 - - - -
100A GLY* 1.3 75.5 - - - +
102A CYS* 1.3 59.1 + - - +
104A GLN* 3.1 8.5 + - - +
105A VAL* 3.0 30.1 + - - +
62B LEU* 3.9 28.0 - - + +
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Residues in contact with CYS 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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65A CYS* 3.5 6.7 - - - -
67A GLU* 3.5 30.7 - - + +
68A ARG* 3.2 35.4 - - - +
71A ILE* 4.9 0.9 - - - +
98A PRO* 4.1 5.4 - - + -
99A CYS* 2.9 7.5 + - - +
101A ALA* 1.3 76.2 - - - +
103A ARG* 1.3 60.7 + - - +
105A VAL* 3.1 2.5 + - - +
106A MET* 2.8 36.6 + - + +
147A ZN 2.4 34.3 - - - -
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Residues in contact with ARG 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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97A SER* 3.8 21.6 + - - -
98A PRO* 2.8 39.8 + - + +
99A CYS 3.1 13.4 + - - +
100A GLY* 3.3 13.4 + - - +
102A CYS* 1.3 75.8 - - - +
104A GLN* 1.3 58.1 + - - +
106A MET* 3.2 13.6 + - - +
107A ARG* 2.8 29.8 + - - +
129A VAL* 4.2 4.6 - - + +
132A LEU* 2.6 67.2 + - + +
133A LEU* 4.0 20.2 - - + +
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Residues in contact with GLN 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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100A GLY 2.9 13.9 + - - +
101A ALA* 3.3 13.0 - - - +
102A CYS 3.1 0.2 - - - -
103A ARG* 1.3 76.0 - - - +
105A VAL* 1.3 64.6 + - + +
107A ARG* 3.5 8.8 + - - +
108A GLU* 3.3 18.9 + - - +
133A LEU* 3.8 21.5 - - + +
137A PHE* 3.1 41.2 + - - +
138A GLY* 5.1 0.2 - - - -
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Residues in contact with VAL 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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68A ARG* 3.7 29.2 - - + +
71A ILE* 4.1 29.8 - - + -
72A GLN* 5.8 5.6 - - + +
101A ALA 3.0 16.9 + - - +
102A CYS 3.8 5.8 - - - +
104A GLN* 1.3 75.7 - - + +
106A MET* 1.3 68.0 + - - +
108A GLU* 3.2 19.8 + - + +
109A PHE* 3.3 15.1 - - + -
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Residues in contact with MET 106 (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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67A GLU* 4.0 24.2 - - + -
71A ILE* 3.8 17.0 - - + -
85A ILE* 4.0 22.7 - - + -
87A ILE* 4.7 0.2 - - + -
98A PRO* 4.0 25.6 - - + -
102A CYS 2.8 21.0 + - - +
103A ARG* 3.3 16.4 - - - +
105A VAL* 1.3 77.3 - - - +
107A ARG* 1.3 63.2 + - - +
109A PHE* 3.0 17.7 + - - +
110A GLY 3.2 9.5 + - - +
113A TRP* 3.7 24.0 + - + -
115A VAL* 3.9 27.4 - - + -
129A VAL* 4.0 9.9 - - + -
132A LEU* 5.4 1.1 - - - -
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Residues in contact with ARG 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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103A ARG 2.8 19.5 + - - +
104A GLN* 3.6 16.6 - - - +
105A VAL 3.3 0.2 - - - -
106A MET* 1.3 68.4 - - - +
108A GLU* 1.3 63.3 + - - +
109A PHE 2.9 6.8 + - - -
110A GLY 3.0 22.3 + - - +
111A THR* 3.3 33.7 - - - +
129A VAL* 3.7 8.9 - - + +
130A GLN* 6.4 0.4 - - - +
133A LEU* 4.1 9.4 - - + -
136A SER* 2.5 32.5 + - - +
137A PHE 3.6 4.3 + - - +
138A GLY* 3.1 19.5 - - - +
139A PRO* 3.8 11.5 - - + +
140A GLU* 2.6 37.4 + - - -
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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 GLN* 3.3 9.8 + - - +
105A VAL* 3.2 16.7 + - - +
106A MET 3.2 0.8 - - - -
107A ARG* 1.3 79.9 - - - +
109A PHE* 1.3 81.4 + - + +
110A GLY 4.1 0.3 + - - -
139A PRO* 3.4 37.1 - - - +
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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