Contacts of the helix formed by residues 97 - 108 (chain A) in PDB entry 4NWO
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 PRO 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A MET* 3.4 14.1 - - + +
96A MET* 1.3 85.3 - - - +
98A GLY* 1.3 62.6 + - - +
99A PHE 3.2 1.4 + - - -
100A GLY* 3.5 3.3 + - - -
101A GLU* 3.2 41.6 + - + +
104A ARG* 4.9 1.4 + - - -
120A THR* 5.8 7.4 - - + -
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Residues in contact with GLY 98 (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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96A MET* 3.1 2.6 - - - +
97A PRO* 1.3 83.3 - - - +
99A PHE* 1.3 63.0 + - - +
101A GLU* 3.9 13.7 - - - +
102A LEU* 3.3 24.8 + - - +
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Residues in contact with PHE 99 (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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96A MET* 3.5 46.2 - - + +
97A PRO 3.2 0.8 + - - -
98A GLY* 1.3 77.0 - - - +
100A GLY* 1.3 66.0 + - - +
102A LEU* 3.3 3.5 + - - +
103A MET* 3.1 36.3 + - + +
121A ALA* 3.6 19.7 - - + -
128A LEU* 4.1 18.8 - - + -
130A VAL* 3.9 26.9 - - + -
146A VAL* 3.7 37.8 - - + +
149A ALA* 5.3 8.3 - - + -
150A ILE* 4.2 15.5 - - + -
153A CYS* 5.5 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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96A MET 4.5 1.0 + - - -
97A PRO 3.5 5.5 + - - -
99A PHE* 1.3 78.1 - - - +
101A GLU* 1.3 61.9 + - - +
103A MET* 3.9 10.3 - - - +
104A ARG* 3.1 43.1 + - - +
119A GLN* 3.6 25.5 + - - -
120A THR* 4.9 4.7 - - - +
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Residues in contact with GLU 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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97A PRO* 3.2 34.9 + - - +
98A GLY* 3.9 10.4 - - - +
99A PHE 3.2 0.8 - - - -
100A GLY* 1.3 78.8 - - - +
102A LEU* 1.3 57.0 + - - +
104A ARG* 3.5 14.5 - - - +
105A ALA* 3.1 27.0 + - - +
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Residues in contact with LEU 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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98A GLY 3.3 16.7 + - - +
99A PHE 3.3 2.9 + - - +
101A GLU* 1.3 76.0 - - - +
103A MET* 1.3 61.0 + - - +
105A ALA* 3.1 11.6 + - + +
106A GLU* 3.0 30.8 + - + +
145A ALA* 3.6 36.1 - - + +
146A VAL* 4.5 7.9 - - + -
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Residues in contact with MET 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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99A PHE* 3.1 41.8 + - + +
100A GLY* 3.9 5.6 - - - +
102A LEU* 1.3 77.8 - - - +
104A ARG* 1.3 60.9 + - - +
106A GLU* 3.4 5.6 + - - +
107A SER* 3.1 29.0 + - - -
119A GLN* 3.8 26.9 - - + +
120A THR 5.3 2.7 - - - +
130A VAL* 4.6 7.2 - - + -
131A ASN 3.7 22.9 - - - +
132A LEU* 4.1 7.4 - - - -
142A CYS* 4.0 41.4 - - - +
145A ALA* 4.9 4.5 - - + -
146A VAL* 3.9 19.1 - - + -
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Residues in contact with ARG 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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97A PRO 4.9 1.0 + - - -
100A GLY* 3.1 36.1 + - - +
101A GLU* 3.5 16.4 - - - +
103A MET* 1.3 78.5 - - - +
105A ALA* 1.3 57.3 + - - +
107A SER* 3.5 3.5 + - - -
108A LEU* 3.1 39.8 + - + +
114A ALA* 3.5 25.4 - - - +
115A ILE* 4.6 7.9 - - - +
117A SER* 3.4 36.6 + - - +
118A ARG* 4.0 3.0 - - - +
119A GLN* 3.2 30.1 + - - +
120A THR* 5.6 3.0 - - - +
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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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101A GLU 3.1 19.2 + - - +
102A LEU* 3.1 16.0 + - + +
104A ARG* 1.3 78.6 - - - +
106A GLU* 1.3 60.7 + - - +
108A LEU* 3.8 16.2 + - - +
109A LYS* 4.1 6.2 + - - +
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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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102A LEU* 3.0 19.1 + - + +
103A MET* 4.0 5.6 - - - +
105A ALA* 1.3 77.4 - - - +
107A SER* 1.3 63.0 + - - +
108A LEU 3.4 0.2 - - - -
109A LYS* 3.8 15.8 + - - +
110A GLU* 4.5 2.1 + - - +
141A ASP 5.7 2.0 - - - +
145A ALA* 4.9 14.4 - - + -
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Residues in contact with SER 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 MET 3.1 17.6 + - - -
104A ARG* 4.1 0.9 - - - -
106A GLU* 1.3 74.9 - - - +
108A LEU* 1.3 60.2 + - - +
109A LYS 3.1 2.5 - - - -
110A GLU* 2.9 22.4 + - - +
111A VAL* 2.9 16.0 + - - +
114A ALA* 3.7 18.6 - - - -
138A SER* 6.0 1.2 - - - -
141A ASP* 6.2 0.3 - - - +
142A CYS* 4.7 12.6 - - - -
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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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104A ARG* 3.1 25.6 + - + +
105A ALA* 4.0 9.9 - - - +
106A GLU 3.4 0.4 - - - -
107A SER* 1.3 73.1 - - - +
109A LYS* 1.3 60.1 + - - +
110A GLU 3.0 11.3 + - - +
111A VAL 3.5 18.7 - - - +
112A PRO* 3.9 22.4 - - + +
114A ALA* 3.8 7.4 - - + +
115A ILE* 4.0 22.2 - - + -
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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