Contacts of the helix formed by residues 119 - 128 (chain N) in PDB entry 4G7H
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 SER 119 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110N SER* 6.2 0.8 - - - -
113N GLY* 5.2 0.6 - - - -
117N ASP 4.3 0.2 - - - -
118N LEU* 1.3 78.2 - - - +
120N ALA* 1.3 63.7 + - - +
121N THR* 3.5 8.6 + - - -
122N GLU* 2.9 39.2 + - - +
123N LEU* 3.2 19.4 + - - +
22R T 5.8 2.5 - - - -
23R G 6.1 0.9 - - - -
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Residues in contact with ALA 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N SER* 6.0 6.3 - - - -
119N SER* 1.3 74.9 - - - +
121N THR* 1.3 59.5 + - - +
123N LEU* 3.9 3.8 - - - +
124N GLU* 2.9 31.3 + - - +
22R T 5.5 9.0 + - - +
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Residues in contact with THR 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119N SER* 3.3 7.3 + - - -
120N ALA* 1.3 80.1 - - - +
122N GLU* 1.3 59.5 + - + +
124N GLU* 3.3 8.3 - - + +
125N GLN* 2.9 54.0 + - + +
23R G 5.8 0.3 + - - -
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Residues in contact with GLU 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N ASP 4.0 3.1 - - - +
118N LEU* 3.2 24.2 - - + +
119N SER* 2.9 35.6 + - - +
121N THR* 1.3 77.7 - - + +
123N LEU* 1.3 57.7 - - - +
125N GLN* 3.0 13.3 + - - +
126N VAL* 2.9 34.2 + - - +
152N LEU* 3.6 26.7 - - + +
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Residues in contact with LEU 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105N VAL* 4.3 16.2 - - + +
110N SER* 3.4 28.7 - - - +
112N ILE* 3.9 23.1 - - + -
113N GLY* 3.6 16.4 - - - +
118N LEU* 4.3 14.1 - - + +
119N SER 3.2 15.2 + - - +
120N ALA* 3.9 4.0 - - - +
122N GLU* 1.3 78.7 - - - +
124N GLU* 1.3 57.0 + - - +
126N VAL* 4.0 2.6 - - - +
127N LEU* 2.9 54.3 + - + +
461N ILE* 4.0 24.7 - - + -
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Residues in contact with GLU 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105N VAL* 5.9 2.6 - - - +
106N LYS* 4.1 14.9 - - - -
120N ALA 2.9 18.7 + - - +
121N THR* 3.3 10.8 - - + +
122N GLU 3.2 0.2 - - - -
123N LEU* 1.3 76.7 - - - +
125N GLN* 1.3 67.2 + - + +
127N LEU* 4.8 0.9 - - - -
128N TYR* 3.0 42.7 + - - +
587N ARG* 2.3 38.9 + - - -
78P SER* 4.8 5.5 + - - -
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Residues in contact with GLN 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121N THR* 2.9 40.3 + - + +
122N GLU* 3.0 12.7 + - - +
124N GLU* 1.3 79.2 - - + +
126N VAL* 1.3 60.6 + - + +
129N PHE 3.4 0.7 + - - -
130N SER* 2.7 48.4 + - - +
131N LYS* 3.1 49.3 + - + +
152N LEU* 4.3 5.3 - - + +
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Residues in contact with VAL 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N LEU* 5.8 1.6 - - + -
122N GLU 2.9 21.1 + - - +
123N LEU* 4.1 3.1 - - - +
125N GLN* 1.3 76.3 - - + +
127N LEU* 1.3 61.4 + - - +
129N PHE* 3.3 9.7 + - - -
131N LYS* 3.7 13.2 - - + +
133N ILE* 4.0 23.8 - - + -
152N LEU* 3.7 28.9 - - + -
456N MET* 4.1 5.0 - - - -
457N GLY 2.6 42.5 + - - +
461N ILE* 3.8 26.7 - - + -
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Residues in contact with LEU 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100N ALA* 3.9 17.3 - - + -
105N VAL* 3.5 43.5 - - + -
112N ILE* 5.6 0.9 - - + -
123N LEU* 2.9 33.9 + - + +
126N VAL* 1.3 77.9 - - - +
128N TYR* 1.3 75.7 + - + +
129N PHE* 3.4 20.0 - - - -
457N GLY* 3.9 4.6 - - - -
458N ALA* 3.7 30.9 + - + +
461N ILE* 3.8 16.4 - - + -
575N GLN* 4.1 14.6 - - - +
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Residues in contact with TYR 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N ILE* 4.5 3.6 - - - +
105N VAL* 5.3 8.4 - - + +
106N LYS* 5.9 0.2 - - - -
124N GLU* 3.0 29.3 + - - +
125N GLN 4.1 0.7 - - - -
127N LEU* 1.3 94.2 - - + +
129N PHE* 1.3 72.6 + - - +
130N SER* 3.4 3.4 + - - -
572N ARG* 3.3 15.0 + - - -
575N GLN* 3.3 30.2 + - + -
576N GLU* 4.3 14.6 - - - -
579N ASP* 2.0 34.6 + - - -
587N ARG* 3.3 58.8 - - - +
83P GLN* 3.2 16.2 + - - +
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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