Contacts of the helix formed by residues 104 - 112 (chain A) in PDB entry 2W3W
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 GLY 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.4 0.2 - - - -
50A THR* 3.4 11.0 - - - -
103A GLY* 1.3 69.9 + - - -
105A ALA* 1.3 60.8 + - - -
106A GLN 3.3 3.1 - - - -
107A ILE* 3.2 0.9 + - - +
108A TYR* 2.8 39.7 + - - -
1169A NDP 2.9 37.8 + - - -
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Residues in contact with ALA 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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18A ILE* 3.7 8.1 - - + +
104A GLY* 1.3 72.2 - - - +
106A GLN* 1.3 63.3 + - + +
108A TYR* 3.5 5.8 + - - +
109A LEU* 3.4 26.5 + - + +
134A ALA* 4.1 10.8 - - + -
135A LEU 3.4 38.3 - - - +
137A PRO* 5.9 0.3 - - - +
1169A NDP 3.2 15.5 + - - +
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Residues in contact with GLN 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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49A ARG* 2.5 36.4 + - - +
71A ARG* 4.7 6.7 - - - +
105A ALA* 1.3 76.4 - - + +
107A ILE* 1.3 64.2 + - - +
109A LEU* 3.2 12.1 + - + +
110A LEU* 3.2 23.2 + - - +
1169A NDP 3.0 58.0 + - + +
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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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45A ILE* 4.6 2.9 - - + +
46A MET* 4.2 3.8 - - - -
47A GLY* 3.5 21.8 - - - +
69A VAL* 4.2 15.5 - - + -
86A LEU* 4.5 10.7 - - + +
101A VAL* 3.3 27.4 - - + -
103A GLY 3.6 21.1 - - - +
104A GLY 3.2 2.2 + - - +
106A GLN* 1.3 76.0 - - - +
108A TYR* 1.3 67.5 + - - +
110A LEU* 3.2 14.1 + - + +
111A ALA* 3.0 20.8 + - - +
1169A NDP 3.2 48.9 + - + +
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Residues in contact with TYR 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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8A LEU* 3.6 26.3 - - + +
9A VAL 2.6 26.7 + - - -
10A TRP* 3.2 23.0 - + + +
18A ILE* 3.8 22.7 - - + -
101A VAL* 3.6 18.6 - - + -
102A ILE 3.1 14.7 + - - -
103A GLY* 3.2 25.6 - - - -
104A GLY 2.8 24.2 + - - +
105A ALA* 3.8 5.2 - - - +
106A GLN 3.3 0.4 - - - -
107A ILE* 1.3 74.9 - - - +
109A LEU* 1.3 57.3 + - - +
111A ALA* 3.2 1.4 + - - +
112A LEU* 2.9 33.0 + - - +
137A PRO* 3.9 33.9 - - + -
1168A VG9 3.5 2.4 + - - -
1169A NDP 3.6 3.4 - + - -
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Residues in contact with LEU 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 ALA* 3.4 15.2 + - + +
106A GLN* 3.2 11.9 + - + +
108A TYR* 1.3 81.7 - - - +
110A LEU* 1.3 61.5 + - - +
111A ALA 3.5 0.2 + - - -
112A LEU* 3.8 12.1 + - + +
113A PRO* 3.6 14.9 - - - +
137A PRO* 4.4 23.6 - - + -
138A ALA 5.5 1.6 - - - +
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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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69A VAL* 4.9 1.8 - - + -
85A SER* 5.9 0.2 - - - -
86A LEU* 3.7 29.8 - - + +
106A GLN 3.2 13.5 + - - +
107A ILE* 3.2 17.2 + - + +
109A LEU* 1.3 76.8 - - - +
111A ALA* 1.3 60.1 + - - +
113A PRO* 3.6 9.1 - - - +
114A HIS* 3.5 17.0 + - - -
1169A NDP 3.4 50.3 - - + +
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Residues in contact with ALA 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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6A VAL* 5.1 2.8 - - + +
8A LEU* 3.9 12.6 - - + -
86A LEU* 3.9 12.3 - - + -
101A VAL* 3.7 30.1 - - + -
107A ILE 3.0 16.2 + - - +
110A LEU* 1.3 73.8 - - - +
112A LEU* 1.3 66.4 + - - +
113A PRO* 3.3 3.8 - - - -
114A HIS* 2.8 25.7 + - + +
115A ALA* 3.3 10.5 + - - +
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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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8A LEU* 3.3 28.9 - - + +
108A TYR 2.9 13.4 + - - +
109A LEU* 4.0 13.5 - - + +
111A ALA* 1.3 77.0 - - - +
113A PRO* 1.4 61.7 - - + +
115A ALA* 3.0 13.2 + - - +
137A PRO* 4.0 19.3 - - + -
138A ALA 3.8 21.5 - - - +
139A LEU* 3.8 21.8 - - + -
140A ASP* 6.1 0.9 - - - +
143A TRP* 4.0 13.2 - - + +
166A ARG* 2.7 23.4 + - - +
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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