Contacts of the helix formed by residues 100 - 109 (chain A) in PDB entry 2H8W
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 THR 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ARG* 3.7 19.3 - - - +
99A ILE* 1.3 90.1 - - - +
101A TRP* 1.3 63.4 + - - +
102A GLU* 3.0 14.2 + - - +
103A GLN* 3.3 30.4 + - - +
104A VAL* 3.7 2.6 + - - +
138A VAL* 6.3 0.4 - - - -
139A VAL* 3.1 13.9 - - + +
140A GLY* 5.2 3.1 - - - -
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Residues in contact with TRP 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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100A THR* 1.3 74.2 - - - +
102A GLU* 1.3 56.9 + - - +
104A VAL* 2.9 32.3 - - + +
105A LEU* 3.1 36.3 - - + +
121A GLU* 3.3 39.1 + - - -
124A ALA* 3.5 36.6 - - + -
125A ARG* 4.1 9.4 - - - -
128A ALA* 3.7 26.7 - - + -
138A VAL* 5.0 4.7 - - + -
139A VAL 2.8 7.5 + - - -
140A GLY* 2.9 31.5 - - - +
141A ALA* 3.5 24.7 - - + -
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Residues in contact with GLU 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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100A THR* 3.0 12.2 - - - +
101A TRP* 1.3 78.3 - - - +
103A GLN* 1.3 75.9 + - - +
105A LEU* 3.5 13.7 + - - +
106A GLU* 3.1 33.0 + - + +
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Residues in contact with GLN 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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80A LYS* 5.3 4.4 - - + +
81A ALA* 3.4 29.6 + - + +
91A PRO* 4.7 23.7 - - - +
99A ILE* 3.6 31.0 - - + -
100A THR* 3.3 20.5 + - - +
102A GLU* 1.3 88.3 - - - +
104A VAL* 1.3 59.3 + - - +
106A GLU* 2.7 45.3 + - - +
107A ILE* 3.4 11.5 + - + +
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Residues in contact with VAL 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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99A ILE* 4.1 10.2 - - + +
100A THR 3.7 3.5 + - - +
101A TRP* 2.9 53.4 - - + +
103A GLN* 1.3 74.6 - - - +
105A LEU* 1.3 57.1 + - + +
107A ILE* 3.3 12.7 + - - +
108A ALA* 3.0 23.2 + - - +
124A ALA* 3.9 14.6 - - + +
127A ILE* 3.6 42.4 - - + +
128A ALA* 4.4 4.0 - - - +
138A VAL* 6.1 3.4 - - + -
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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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101A TRP* 3.1 44.6 - - + +
102A GLU* 3.5 17.9 + - - +
103A GLN 3.1 0.4 - - - -
104A VAL* 1.3 73.2 - - + +
106A GLU* 1.3 63.2 + - - +
107A ILE 2.9 6.6 + - - -
108A ALA* 4.1 0.2 - - - -
109A LYS* 3.1 23.7 + - - +
120A LEU* 3.2 50.4 - - + +
121A GLU* 4.1 4.7 - - + +
124A ALA* 3.2 31.2 - - + -
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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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80A LYS* 3.7 28.7 + - - +
91A PRO* 6.2 0.3 - - - +
102A GLU* 3.1 28.3 + - + +
103A GLN* 2.7 27.9 + - - +
105A LEU* 1.3 76.1 - - - +
107A ILE* 1.3 59.7 + - - +
109A LYS* 4.4 11.8 - - - +
110A GLN* 4.8 5.9 + - - +
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Residues in contact with ILE 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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74A ALA* 4.9 5.6 - - + +
77A LEU* 3.2 63.4 - - + +
78A ILE* 4.3 11.2 - - + +
80A LYS* 3.3 24.7 - - - +
81A ALA* 4.6 9.4 - - + -
99A ILE* 6.2 0.2 - - + -
103A GLN 3.4 24.7 - - - +
104A VAL* 3.3 8.4 + - - +
105A LEU 2.9 0.2 - - - -
106A GLU* 1.3 77.4 - - - +
108A ALA* 1.3 67.1 + - - +
109A LYS 3.0 3.5 + - - -
110A GLN* 3.2 8.4 + - - +
111A LYS* 3.1 20.7 + - + +
127A ILE* 5.6 8.7 - - + -
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Residues in contact with ALA 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 VAL 3.0 17.4 + - - +
105A LEU* 4.1 1.3 - - - -
107A ILE* 1.3 77.0 - - - +
109A LYS* 1.3 65.3 + - - +
111A LYS* 2.9 21.2 + - - +
112A MET* 3.0 15.7 - - - +
120A LEU* 3.6 19.1 - - + -
123A ALA* 4.2 12.5 - - + +
124A ALA* 4.3 7.0 - - + -
127A ILE* 4.2 22.6 - - + +
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Residues in contact with LYS 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 3.1 13.1 + - - +
106A GLU* 4.4 8.5 - - - +
108A ALA* 1.3 79.4 - - - +
110A GLN* 1.3 64.3 + - + +
111A LYS 3.0 0.3 + - - -
112A MET* 3.2 25.6 + - + +
120A LEU* 3.2 40.3 - - + +
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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