Contacts of the helix formed by residues 115 - 128 (chain A) in PDB entry 1IN5
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 ASN 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY 5.0 0.2 + - - -
87A LEU 3.0 17.0 + - - -
88A VAL* 2.6 35.5 + - - +
113A ARG 3.5 5.0 + - - +
114A LEU* 1.3 73.4 - - - +
116A LYS* 1.3 83.4 + - - +
117A ALA* 3.1 10.4 + - - +
118A VAL* 2.8 23.7 + - - +
119A GLU* 2.8 17.3 + - - +
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Residues in contact with LYS 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 LEU 3.7 1.2 + - - -
115A ASN* 1.3 91.7 - - - +
117A ALA* 1.3 66.7 + - + +
119A GLU* 4.0 7.9 - - - -
120A GLU* 2.9 37.2 + - + +
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Residues in contact with ALA 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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88A VAL 4.2 8.1 - - - +
89A LYS* 5.5 0.4 - - - -
90A GLN* 3.1 40.7 + - + +
115A ASN* 3.0 13.2 + - - +
116A LYS* 1.3 88.5 - - + +
118A VAL* 1.3 60.9 + - - +
120A GLU* 3.4 7.5 + - - +
121A LEU 3.4 3.3 + - - -
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Residues in contact with VAL 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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87A LEU* 3.6 23.1 - - + +
88A VAL 3.6 19.5 - - - +
89A LYS 3.7 22.0 - - - +
90A GLN* 3.9 2.7 - - - +
93A MET* 3.8 25.1 - - + +
114A LEU* 3.7 22.7 - - + -
115A ASN* 2.8 27.0 + - - +
117A ALA* 1.3 71.8 - - - +
119A GLU* 1.3 62.4 + - - +
121A LEU* 3.3 8.6 + - - +
122A LEU* 2.9 30.9 + - - +
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Residues in contact with GLU 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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114A LEU* 4.0 22.0 - - + +
115A ASN 2.8 22.1 + - - +
116A LYS* 3.7 7.0 - - - +
118A VAL* 1.3 80.3 - - - +
120A GLU* 1.3 77.2 + - - +
122A LEU* 3.3 5.9 + - - +
123A TYR* 2.9 31.4 + - - +
164A SER* 3.1 27.6 + - - +
166A PRO* 4.7 4.1 - - - +
167A LEU* 3.4 30.2 + - + +
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Residues in contact with GLU 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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90A GLN* 5.0 4.0 - - - +
116A LYS* 2.9 32.5 + - + +
117A ALA* 3.7 4.7 - - - +
119A GLU* 1.3 97.7 + - - +
121A LEU* 1.3 58.5 + - - +
123A TYR* 3.5 10.7 + - - +
124A SER* 3.0 28.8 + - - -
166A PRO* 6.1 1.2 - - - +
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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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90A GLN* 3.6 47.3 - - + +
93A MET* 3.8 17.3 - - + -
94A ALA* 3.8 15.3 - - + +
97A LEU* 4.3 3.1 - - + -
117A ALA 3.4 9.6 + - - +
118A VAL* 3.3 8.7 + - - +
119A GLU 3.3 0.2 - - - -
120A GLU* 1.3 77.7 - - - +
122A LEU* 1.3 65.0 + - - +
124A SER* 3.2 8.6 - - - -
125A ALA* 3.0 22.7 + - - +
131A ILE* 3.6 31.8 - - + +
132A ASP* 4.3 13.0 - - + +
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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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93A MET* 3.6 20.4 - - + +
97A LEU* 4.4 10.8 - - + -
106A LEU* 4.0 23.3 - - + -
108A ILE* 3.8 13.9 - - + -
111A ILE* 4.4 2.5 - - + -
114A LEU* 3.6 28.5 - - + -
118A VAL 2.9 17.4 + - - +
119A GLU* 3.6 4.9 - - - +
121A LEU* 1.3 74.3 - - - +
123A TYR* 1.3 66.3 + - - +
125A ALA* 3.1 12.0 + - - +
126A ILE* 3.0 28.3 + - + +
153A LEU* 4.3 21.3 - - + -
167A LEU* 4.4 12.3 - - + -
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Residues in contact with TYR 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 GLU* 2.9 25.3 + - - +
120A GLU* 3.7 11.2 - - - +
122A LEU* 1.3 76.1 - - - +
124A SER* 1.3 64.9 + - - +
126A ILE* 3.2 9.4 + - - +
127A GLU* 3.1 50.1 + - + +
166A PRO* 3.4 44.9 + - + +
167A LEU* 4.0 10.9 - - + +
169A SER* 5.3 2.3 + - - -
170A ARG* 3.4 25.4 - - + -
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Residues in contact with SER 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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120A GLU 3.0 14.8 + - - -
121A LEU* 3.2 15.5 - - - -
122A LEU 3.1 0.2 - - - -
123A TYR* 1.3 75.8 - - - +
125A ALA* 1.3 59.7 + - - +
126A ILE 3.0 9.5 + - - -
127A GLU* 3.1 16.0 + - - +
128A ASP* 3.6 16.7 + - - +
130A GLN 3.4 16.2 + - - -
131A ILE* 4.1 7.8 - - - -
132A ASP 4.4 4.0 + - - -
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Residues in contact with ALA 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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97A LEU* 3.8 31.9 - - + -
121A LEU 3.0 13.7 + - - +
122A LEU 3.1 8.5 + - - +
124A SER* 1.3 75.1 + - - +
126A ILE* 1.3 58.3 + - - +
129A PHE* 2.9 35.2 + - - -
130A GLN 4.0 11.0 - - - +
131A ILE* 4.1 8.3 - - + +
148A ILE* 4.5 9.4 - - + -
151A PHE* 4.3 5.5 - - + -
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Residues in contact with ILE 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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53A HIS* 3.2 39.4 + - + +
122A LEU* 3.0 20.9 - - + +
123A TYR* 3.4 9.4 - - - +
124A SER 3.0 1.0 - - - -
125A ALA* 1.3 79.3 - - - +
127A GLU* 1.3 63.3 + - - +
128A ASP 3.3 1.0 + - - -
129A PHE* 4.4 13.7 - - + -
151A PHE* 3.4 37.9 - - + -
153A LEU* 4.3 19.3 - - + -
167A LEU* 5.3 2.2 - - + -
170A ARG* 3.2 34.2 + - + +
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Residues in contact with GLU 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 TYR* 3.1 48.2 + - + +
124A SER* 3.1 10.4 + - - +
126A ILE* 1.3 79.5 - - - +
128A ASP* 1.3 68.2 + - - +
129A PHE* 5.5 0.2 - - - -
170A ARG* 2.9 33.4 + - - +
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Residues in contact with ASP 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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124A SER* 3.6 6.6 + - - +
126A ILE 3.3 0.2 - - - -
127A GLU* 1.3 84.7 - - - +
129A PHE* 1.3 80.0 + - - +
130A GLN* 3.1 38.1 + - - +
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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