Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 3HIC
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLU* 3.1 31.2 + - - -
112A THR* 3.7 2.3 + - - -
113A VAL* 1.3 76.6 - - - +
115A GLN* 1.3 65.2 + - - +
116A THR* 3.5 12.4 + - - -
117A ASN* 2.9 27.7 + - - +
118A LYS* 3.0 11.7 + - - +
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Residues in contact with GLN 115 (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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113A VAL 3.8 0.8 + - - -
114A SER* 1.3 72.7 - - - +
116A THR* 1.3 57.1 + - - +
118A LYS* 3.8 31.1 + - - +
119A ASP* 2.9 63.3 + - - +
122A LEU* 6.0 0.2 - - - +
149A ASP* 4.6 7.2 + - - +
152A GLU* 5.1 7.7 + - - -
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Residues in contact with THR 116 (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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114A SER* 3.5 12.4 + - - -
115A GLN* 1.3 80.9 - - - +
117A ASN* 1.3 59.5 + - - +
119A ASP* 3.5 6.8 + - - +
120A ASN* 2.9 41.5 + - - +
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Residues in contact with ASN 117 (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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59A ILE* 4.1 9.5 - - + +
82A LEU* 3.4 27.9 - - - +
83A VAL 3.2 26.7 + - - +
84A GLU* 2.5 38.0 + - - +
113A VAL* 3.7 13.2 - - + -
114A SER* 2.9 6.1 + - - +
116A THR* 1.3 79.9 - - - +
118A LYS* 1.3 65.3 + - - +
119A ASP 3.1 1.3 - - - -
120A ASN* 3.6 16.1 + - - +
121A LEU* 3.0 20.6 + - - +
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Residues in contact with LYS 118 (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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59A ILE* 5.8 1.1 - - - -
113A VAL* 3.4 34.6 + - + -
114A SER 3.0 14.9 + - - +
115A GLN* 3.7 30.6 + - - +
117A ASN* 1.3 77.2 - - - +
119A ASP* 1.3 63.7 + - - +
121A LEU* 3.2 14.1 + - - +
122A LEU* 3.3 19.8 + - + +
144A HIS* 3.0 21.5 + - - +
145A TYR* 4.0 29.8 + - + +
146A THR* 5.5 0.2 - - - +
149A ASP* 2.8 37.6 + - + +
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Residues in contact with ASP 119 (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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115A GLN* 2.9 46.6 + - - +
116A THR* 3.7 6.4 - - - +
118A LYS* 1.3 80.2 - - - +
120A ASN* 1.3 63.8 + - - +
122A LEU* 3.2 19.2 + - - +
123A LYS* 3.0 23.0 + - - +
152A GLU* 5.3 2.1 - - - +
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Residues in contact with ASN 120 (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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82A LEU* 3.7 26.1 - - + +
116A THR* 2.9 34.9 + - - +
117A ASN* 3.2 15.6 + - - +
119A ASP* 1.3 76.5 - - - +
121A LEU* 1.3 56.7 + - - +
123A LYS* 3.4 31.8 + - - +
124A GLN* 2.9 32.0 + - + +
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Residues in contact with LEU 121 (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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5A ILE* 4.4 6.5 - - + -
7A LEU* 3.5 31.4 - - + -
57A LEU* 4.4 22.0 - - + -
58A GLY* 4.5 9.2 - - - +
59A ILE* 4.3 10.1 - - + -
82A LEU* 3.4 12.1 - - + +
117A ASN 3.0 12.1 + - - +
118A LYS* 3.4 10.1 - - - +
119A ASP 3.1 0.2 - - - -
120A ASN* 1.3 74.7 - - - +
122A LEU* 1.3 65.3 + - + +
124A GLN* 3.1 28.1 + - - +
125A ILE* 3.1 20.6 + - + +
145A TYR* 4.2 7.2 - - + +
153A LEU* 3.7 23.8 - - + -
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Residues in contact with LEU 122 (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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115A GLN* 6.0 0.2 - - - +
118A LYS* 3.4 16.8 - - + +
119A ASP* 3.2 20.1 + - - +
121A LEU* 1.3 77.7 - - + +
123A LYS* 1.3 61.4 + - - +
125A ILE* 3.4 3.2 + - - -
126A ALA* 3.2 19.4 + - - +
145A TYR* 5.3 3.4 - - - +
149A ASP 5.3 0.4 - - - +
152A GLU* 3.9 30.3 - - + +
153A LEU* 3.7 35.9 - - + +
156A THR* 3.5 39.5 - - + +
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Residues in contact with LYS 123 (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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119A ASP 3.0 14.5 + - - +
120A ASN* 3.4 31.1 + - - +
121A LEU 3.2 0.2 - - - -
122A LEU* 1.3 75.4 - - - +
124A GLN* 1.3 66.3 + - + +
126A ALA* 3.3 6.7 + - + +
127A LYS* 2.9 52.0 + - + +
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Residues in contact with GLN 124 (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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57A LEU* 4.5 11.7 - - + +
58A GLY 5.1 0.3 - - - +
80A ASP* 3.1 43.9 + - - +
81A PHE 5.0 0.2 - - - -
82A LEU* 3.4 38.9 - - + +
120A ASN 2.9 15.3 + - - +
121A LEU* 3.1 18.6 + - - +
123A LYS* 1.3 79.2 - - + +
125A ILE* 1.3 56.8 + - - +
127A LYS* 4.6 4.0 - - - -
128A LYS* 2.9 53.9 + - + +
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Residues in contact with ILE 125 (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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5A ILE* 3.8 20.6 - - + -
57A LEU* 4.6 10.8 - - + -
121A LEU* 3.1 19.5 + - + +
122A LEU* 3.6 9.6 - - - +
123A LYS 3.2 0.2 - - - -
124A GLN* 1.3 78.1 - - - +
126A ALA* 1.3 57.8 + - - +
128A LYS* 4.9 0.2 - - - -
129A VAL* 3.0 49.0 + - + +
135A VAL* 5.9 0.4 - - + -
153A LEU* 3.5 33.9 - - + +
156A THR* 3.9 25.8 - - + +
157A VAL* 4.0 17.3 - - + -
160A THR* 3.9 8.1 - - + +
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Residues in contact with ALA 126 (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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122A LEU 3.2 13.6 + - - +
123A LYS* 3.3 9.8 + - - +
125A ILE* 1.3 78.3 - - - +
127A LYS* 1.3 69.0 + - + +
129A VAL 4.5 6.6 - - - +
130A LYS* 5.4 1.0 + - - -
156A THR* 5.0 6.3 - - + -
160A THR* 4.7 8.8 - - - +
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Residues in contact with LYS 127 (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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123A LYS* 2.9 41.8 + - + +
124A GLN* 3.9 5.6 - - - +
126A ALA* 1.3 84.6 - - - +
128A LYS* 1.3 62.3 + - + +
130A LYS* 3.5 14.4 + - - -
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Residues in contact with LYS 128 (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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3A TYR* 3.6 27.8 + - + +
55A GLU* 2.8 29.6 + - - +
57A LEU* 4.3 11.2 - - + -
80A ASP* 2.8 30.3 + - - -
124A GLN* 2.9 44.4 + - + +
127A LYS* 1.3 84.4 - - + +
129A VAL* 1.3 66.6 + - + +
130A LYS* 3.1 19.4 + - - +
133A ASP* 3.9 1.2 - - - +
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Residues in contact with VAL 129 (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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3A TYR* 4.0 16.4 - - + -
57A LEU* 5.6 1.6 - - + -
125A ILE* 3.0 43.7 + - + +
126A ALA 4.5 5.5 - - - +
128A LYS* 1.3 72.6 - - + +
130A LYS* 1.3 67.8 + - - +
133A ASP* 3.6 8.1 - - + +
135A VAL* 3.8 23.6 - - + -
157A VAL* 5.3 0.2 - - + -
160A THR* 3.3 38.8 - - + +
162A ALA* 3.4 20.9 - - + -
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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