Contacts of the helix formed by residues 100 - 114 (chain A) in PDB entry 1JH9
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ALA 2.7 19.3 + - - +
98A TRP* 4.2 4.0 - - + +
99A ASN* 1.3 71.0 - - - +
101A LEU* 1.3 57.4 + - - +
102A GLU* 3.4 17.6 - - - +
103A LYS* 2.9 39.9 + - + +
104A GLN* 2.7 38.7 + - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ASN 3.8 3.6 + - - -
100A ASN* 1.3 73.3 - - - +
102A GLU* 1.3 52.7 + - - +
104A GLN* 2.7 26.8 + - - +
105A ARG* 2.7 32.2 + - + +
127A PRO* 5.9 2.9 - - + -
129A PRO* 3.5 35.9 - - + +
130A LEU* 4.3 10.5 - - + +
133A MET* 3.6 27.4 - - + -
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Residues in contact with GLU 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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100A ASN* 3.3 15.0 - - - +
101A LEU* 1.3 80.2 - - - +
103A LYS* 1.3 62.7 + - - +
105A ARG* 2.8 50.2 + - - +
106A ALA* 2.7 38.7 + - - +
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Residues in contact with LYS 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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96A ASN 4.6 0.6 + - - -
97A ALA* 3.6 19.5 - - - +
98A TRP* 3.5 25.6 - - - +
100A ASN* 2.9 37.4 + - + +
102A GLU* 1.3 86.4 + - - +
104A GLN* 1.3 57.2 + - - +
106A ALA* 3.3 5.0 + - + +
107A TYR* 3.0 60.1 + - + +
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Residues in contact with GLN 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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65A LEU* 4.4 6.0 - - + +
97A ALA* 3.2 19.8 - - + +
99A ASN* 3.6 25.7 + - - +
100A ASN 2.7 14.9 + - - +
101A LEU* 2.7 40.0 + - - +
103A LYS* 1.3 76.7 - - - +
105A ARG* 1.3 62.7 + - - +
107A TYR* 3.4 3.1 + - - +
108A LEU* 2.9 29.6 + - - +
123A CYS* 4.3 21.8 - - - +
125A GLU 5.2 1.6 - - - +
130A LEU* 3.8 21.9 - - + +
133A MET* 3.2 10.3 - - + +
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Residues in contact with ARG 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 LEU* 2.7 10.6 + - + +
102A GLU* 2.8 60.7 + - - +
104A GLN* 1.3 77.4 - - - +
106A ALA* 1.3 75.4 + - - +
108A LEU* 3.8 2.2 - - - +
109A SER* 3.1 25.5 + - - -
133A MET* 3.0 31.6 - - + +
137A TYR* 4.7 2.1 + - - -
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Residues in contact with ALA 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 GLU* 2.7 27.8 + - - +
103A LYS* 3.6 8.3 - - + +
105A ARG* 1.3 88.6 - - - +
107A TYR* 1.3 58.4 + - + +
109A SER* 4.1 5.3 + - - -
110A MET* 3.0 41.4 + - - +
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Residues in contact with TYR 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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65A LEU* 3.5 21.1 - - + -
93A ILE* 6.0 1.6 - - + -
94A LEU 4.4 5.4 + - - -
95A GLY* 3.4 25.1 - - - -
96A ASN* 3.4 29.0 + - - +
97A ALA* 4.2 9.6 - - + -
103A LYS* 3.0 42.8 + - + +
104A GLN 3.9 0.4 - - - +
106A ALA* 1.3 76.5 - - + +
108A LEU* 1.3 68.6 + - - +
109A SER 3.1 1.8 - - - -
110A MET* 3.6 21.6 - - + +
111A MET* 2.8 39.8 + - + +
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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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65A LEU* 3.3 29.6 - - + -
104A GLN 2.9 19.0 + - - +
105A ARG* 3.8 4.3 - - - +
107A TYR* 1.3 78.7 - - - +
109A SER* 1.3 56.4 + - - +
111A MET* 3.4 5.6 + - - +
112A ALA* 2.9 22.9 + - - +
119A LEU* 3.7 30.8 - - + +
121A VAL* 5.9 0.4 - - + -
130A LEU* 4.9 1.6 - - + -
133A MET* 3.7 22.2 - - + +
134A LEU* 4.1 23.3 - - + -
137A TYR* 3.4 42.1 - - + -
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Residues in contact with SER 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 ARG* 3.1 18.5 + - - -
106A ALA* 4.1 5.4 + - - -
107A TYR 3.1 0.2 - - - -
108A LEU* 1.3 75.2 - - - +
110A MET* 1.3 71.8 + - - +
111A MET 2.9 1.5 + - - -
112A ALA* 3.0 2.6 + - - +
113A GLN* 2.9 44.3 + - - +
137A TYR* 3.7 18.3 + - - -
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Residues in contact with MET 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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106A ALA* 3.0 30.2 + - - +
107A TYR* 3.6 24.2 - - + +
109A SER* 1.3 84.1 + - - +
111A MET* 1.3 57.8 + - + +
113A GLN* 3.9 7.9 - - - +
114A LYS* 3.0 34.6 + - + +
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Residues in contact with MET 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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63A GLY* 4.1 9.2 - - - -
64A LEU 3.8 32.3 - - - +
65A LEU* 4.5 12.3 - - - -
93A ILE* 3.9 24.2 - - + +
95A GLY* 4.2 12.8 - - - +
107A TYR* 2.8 33.6 + - + +
108A LEU* 3.4 7.4 - - - +
110A MET* 1.3 77.4 - - + +
112A ALA* 1.3 66.4 + - - +
114A LYS* 3.1 7.7 + - - +
115A ARG 2.9 15.6 + - - -
116A VAL* 3.3 19.7 + - + +
119A LEU* 3.6 33.9 - - + -
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Residues in contact with ALA 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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108A LEU 2.9 17.8 + - - +
109A SER* 3.0 3.3 + - - +
111A MET* 1.3 74.4 - - - +
113A GLN* 1.3 60.0 + - + +
115A ARG* 2.7 38.9 + - - +
116A VAL* 4.7 5.1 - - - +
119A LEU* 5.9 1.3 - - + +
137A TYR* 3.6 25.1 - - + -
139A HIS* 5.3 6.3 - - + -
140A ILE* 4.9 10.8 - - + -
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Residues in contact with GLN 113 (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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109A SER* 2.9 35.6 + - - +
110A MET* 3.9 7.0 - - - +
112A ALA* 1.3 72.6 - - + +
114A LYS* 1.3 59.5 + - + +
115A ARG* 2.8 35.2 + - - +
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Residues in contact with LYS 114 (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 THR* 3.6 11.3 - - - +
61A SER* 5.2 0.7 + - - -
93A ILE* 4.6 20.6 - - + -
110A MET* 3.0 21.7 + - + +
111A MET* 3.3 8.7 - - - +
113A GLN* 1.3 75.9 - - - +
115A ARG* 1.3 66.3 + - - +
116A VAL* 3.6 8.1 + - + +
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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