Contacts of the helix formed by residues 100 - 116 (chain H) in PDB entry 3JCK
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 ASP 100 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98H GLU* 3.4 22.7 + - - +
99H SER* 1.3 66.2 - - - +
101H LYS* 1.3 59.0 + - + +
102H LYS 2.9 5.2 - - - -
103H SER* 2.7 33.5 + - - +
104H LYS* 3.0 16.0 + - + +
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Residues in contact with LYS 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PHE* 4.9 17.2 - - - -
63H GLU* 3.6 39.5 - - + +
64H VAL* 6.3 0.4 - - - -
67H LEU* 3.9 30.7 - - + -
89H TYR* 4.4 2.0 - - - -
99H SER* 4.1 2.5 - - - +
100H ASP* 1.3 79.9 - - + +
102H LYS* 1.3 49.7 + - - +
104H LYS* 3.5 22.7 - - + +
105H LEU* 2.4 43.9 + - + +
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Residues in contact with LYS 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H TYR* 3.3 36.4 + - + -
97H SER* 3.4 29.8 - - - +
98H GLU 3.8 11.2 - - - -
99H SER 2.6 17.7 + - - +
100H ASP* 5.6 0.4 - - - +
101H LYS* 1.3 68.0 - - - +
103H SER* 1.3 79.4 + - - +
105H LEU* 2.6 25.1 + - - -
106H ILE* 2.8 41.2 + - + +
142H LEU* 6.1 0.8 - - - +
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Residues in contact with SER 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ASP* 2.7 23.1 + - - -
102H LYS* 1.3 92.3 - - - +
104H LYS* 1.3 60.3 + - - -
106H ILE* 4.8 1.5 - - - +
107H SER* 3.2 22.0 + - - -
140H SER* 4.8 4.5 + - - -
141H LEU* 3.3 22.3 - - - +
142H LEU* 3.8 13.8 - - - +
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Residues in contact with LYS 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H LEU* 3.9 30.4 - - + +
100H ASP* 3.0 14.5 + - + +
101H LYS* 3.5 30.1 - - + +
103H SER* 1.3 76.8 - - - +
105H LEU* 1.3 64.4 + - + +
107H SER* 3.6 2.6 + - - -
108H LEU* 3.0 27.8 + - - +
141H LEU* 3.8 14.1 - - + +
172H SER* 5.0 16.7 + - - -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H GLU* 4.7 15.3 - - + +
66H ALA* 4.0 25.1 - - + -
67H LEU* 5.0 10.5 - - + -
78H PHE* 5.0 7.2 - - + -
82H PHE* 4.6 13.5 - - + -
85H LEU* 3.8 27.6 - - + -
89H TYR* 5.3 3.4 - - + +
101H LYS* 2.4 36.8 + - + +
102H LYS* 2.6 11.7 + - - +
104H LYS* 1.3 72.6 - - + +
106H ILE* 1.3 65.6 + - + +
108H LEU* 3.0 30.2 + - + +
109H TYR* 2.9 18.8 + - + +
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H PHE* 4.0 27.1 - - + -
89H TYR* 5.5 3.8 - - + -
90H PHE* 4.2 23.8 - - + -
102H LYS* 2.8 48.4 + - + +
103H SER* 4.8 2.2 - - - +
105H LEU* 1.3 71.4 - - + +
107H SER* 1.3 55.8 + - - +
109H TYR* 2.5 25.4 + - + +
110H LEU* 2.9 16.9 + - + +
129H LEU* 4.0 28.3 - - + -
133H ILE* 4.9 11.2 - - + -
142H LEU* 4.3 17.3 - - + -
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Residues in contact with SER 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H SER 3.2 15.0 + - - -
104H LYS 3.6 9.1 + - - -
105H LEU 3.3 0.8 - - - -
106H ILE* 1.3 78.0 - - - +
108H LEU* 1.3 63.6 + - - +
110H LEU* 3.5 4.6 + - - +
111H LEU* 3.0 26.0 + - - +
141H LEU* 3.8 11.7 - - - +
142H LEU* 3.2 30.3 + - - +
144H TYR* 5.9 1.3 - - - -
145H PRO* 4.0 24.4 - - - +
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Residues in contact with LEU 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H ALA 5.6 0.2 - - - +
67H LEU* 5.4 1.8 - - + -
70H ILE* 3.4 38.1 - - + -
78H PHE* 4.5 9.6 - - + -
104H LYS 3.0 15.5 + - - +
105H LEU* 3.0 30.7 - - + +
107H SER* 1.3 77.4 - - - +
109H TYR* 1.3 54.3 + - - +
111H LEU* 3.3 4.1 + - + +
112H ASN* 2.9 38.2 + - - +
172H SER* 6.1 0.9 - - - +
174H PHE* 4.2 20.4 - - + +
177H PHE* 3.4 33.9 - - + -
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Residues in contact with TYR 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H PHE* 4.6 3.8 - + + -
79H GLU* 3.7 35.0 - - + +
82H PHE* 3.3 57.4 - + + -
83H ASN* 4.3 9.4 + - - -
86H LYS* 4.5 1.8 + - - -
105H LEU* 2.9 9.6 + - + +
106H ILE* 2.5 15.8 + - + +
108H LEU* 1.3 69.1 - - - +
110H LEU* 1.3 74.7 + - + +
112H ASN* 2.9 37.5 + - + +
113H LEU* 3.0 33.2 + - + +
121H LYS* 3.8 23.2 - - - -
125H GLU* 4.0 15.2 + - + -
129H LEU* 6.4 0.2 - - + -
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ILE* 2.9 22.0 + - + +
107H SER* 3.8 6.5 - - - +
109H TYR* 1.3 81.1 - - + +
111H LEU* 1.3 66.1 + - - +
113H LEU* 2.8 18.6 + - + +
114H LEU* 3.0 13.3 + - - +
122H PHE* 3.7 26.3 - - + +
125H GLU* 3.9 22.7 - - + -
126H LEU* 4.9 3.8 - - + -
129H LEU* 3.9 32.1 - - + -
142H LEU* 4.9 8.3 - - + -
145H PRO* 3.8 22.4 - - + -
146H ILE* 4.3 17.5 - - + -
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Residues in contact with LEU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H SER 3.0 18.3 + - - +
108H LEU* 3.6 7.0 - - + +
110H LEU* 1.3 76.3 - - - +
112H ASN* 1.3 63.0 + - - +
114H LEU* 3.1 9.9 + - + +
115H SER* 2.9 18.6 + - - -
144H TYR* 3.3 38.8 - - + -
145H PRO* 4.1 10.2 - - + +
148H LEU* 4.6 4.9 - - + -
174H PHE* 4.7 11.9 - - + +
177H PHE* 3.4 40.8 - - + -
181H LEU* 3.7 24.5 - - + -
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Residues in contact with ASN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H PHE* 5.7 4.3 - - + -
78H PHE* 2.9 35.9 - - - -
79H GLU* 4.7 13.4 - - - +
108H LEU 2.9 25.2 + - - +
109H TYR* 2.9 25.3 + - + +
111H LEU* 1.3 75.9 - - - +
113H LEU* 1.3 56.8 + - + +
115H SER* 2.1 37.6 + - - +
116H GLN* 3.0 10.8 + - + +
177H PHE* 2.9 35.8 - - + -
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Residues in contact with LEU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H GLU* 4.2 18.8 - - - +
109H TYR* 3.4 44.4 - - + +
110H LEU* 2.8 16.6 + - - +
112H ASN* 1.3 73.0 - - - +
114H LEU* 1.3 63.6 + - - +
116H GLN* 3.4 9.1 + - + +
118H ASN* 3.2 40.7 + - + +
121H LYS* 3.9 23.8 - - + -
122H PHE* 4.0 15.9 - - + -
125H GLU* 3.6 20.2 - - + -
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Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H LEU 3.0 6.2 + - - +
111H LEU* 3.5 11.0 - - + +
113H LEU* 1.3 78.2 - - - +
115H SER* 1.3 59.3 + - - +
117H ASN* 2.8 28.8 + - - +
118H ASN 5.1 2.0 - - - +
119H THR* 5.9 2.9 - - + -
122H PHE* 3.5 39.7 - - + -
145H PRO* 3.6 29.2 - - + +
148H LEU* 3.6 23.3 - - + -
149H ASP* 3.9 21.5 - - + +
152H LEU* 5.8 3.6 - - + -
181H LEU* 4.2 14.0 - - + +
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Residues in contact with SER 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H LEU* 2.9 12.4 + - - -
112H ASN* 2.1 40.0 + - - +
114H LEU* 1.3 72.6 - - - +
116H GLN* 1.3 70.8 + - - +
117H ASN* 3.3 6.6 + - - +
177H PHE* 4.7 10.3 - - - -
180H ILE* 4.0 34.3 - - - +
181H LEU* 3.6 22.1 - - - +
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Residues in contact with GLN 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H PHE* 4.8 17.0 - - - +
79H GLU* 5.4 7.4 - - - +
112H ASN* 3.0 15.2 + - + +
113H LEU* 4.0 7.2 - - + +
114H LEU 3.1 0.4 - - - -
115H SER* 1.3 88.3 + - - +
117H ASN* 1.3 69.7 - - - +
118H ASN* 3.1 9.8 + - + +
177H PHE* 6.2 0.2 - - - -
180H ILE* 5.5 5.9 - - - +
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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