Contacts of the helix formed by residues 98 - 113 (chain H) in PDB entry 6CP3
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 GLN 98 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95H SER 4.5 10.4 + - - +
97H SER* 1.3 80.7 - - - +
99H GLU* 1.3 59.8 + - - +
100H ASN* 4.4 13.7 + - + +
101H ILE* 3.2 23.6 + - + +
102H LYS* 3.0 30.2 + - - +
137H LEU* 5.5 1.1 - - - -
24I SER 4.4 4.1 + - - +
25I LEU 5.3 2.5 + - - +
26I LYS* 4.9 14.2 - - - +
27I THR* 4.7 12.8 + - - +
28I GLU* 6.1 1.8 - - - +
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Residues in contact with GLU 99 (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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98H GLN* 1.3 69.8 - - - +
100H ASN* 1.3 62.7 + - - +
102H LYS* 3.4 8.3 - - - -
103H ASN* 2.9 50.1 + - - +
137H LEU* 3.4 48.3 - - + +
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Residues in contact with ASN 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H GLN* 3.2 11.8 + - + +
99H GLU* 1.3 80.6 - - - +
101H ILE* 1.3 68.9 + - + +
104H LEU* 3.3 42.5 - - + +
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Residues in contact with ILE 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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98H GLN* 3.2 26.1 + - + +
100H ASN* 1.3 85.5 - - + +
102H LYS* 1.3 65.0 + - - +
104H LEU* 6.4 0.2 - - + -
105H LEU* 3.3 34.7 + - + +
23I SER 3.3 26.7 - - - +
24I SER* 4.1 10.1 - - - -
25I LEU 4.3 15.3 - - - +
27I THR* 5.3 15.3 - - + +
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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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97H SER* 3.6 31.1 + - - -
98H GLN 3.0 19.2 + - - +
99H GLU* 3.1 10.0 + - + +
101H ILE* 1.3 77.6 - - - +
103H ASN* 1.3 60.1 + - - +
105H LEU* 3.7 1.0 - - - +
106H ALA* 2.8 37.5 + - - +
130H LEU* 3.9 25.6 - - + +
133H LEU* 3.3 44.5 + - + +
136H VAL* 4.9 0.8 - - - +
137H LEU* 3.3 41.4 - - + +
24I SER* 4.3 9.2 - - - -
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Residues in contact with ASN 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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99H GLU* 2.9 42.3 + - - +
100H ASN* 5.7 0.2 - - - -
102H LYS* 1.3 74.8 - - - +
104H LEU* 1.3 65.4 + - + +
106H ALA* 3.5 8.3 - - - +
107H GLU* 3.0 38.2 + - + +
134H GLN* 5.5 4.5 + - - -
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Residues in contact with LEU 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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100H ASN* 3.3 34.2 + - + +
101H ILE* 6.4 0.2 - - + -
102H LYS 3.4 0.4 - - - -
103H ASN* 1.3 80.8 - - + +
105H LEU* 1.3 67.2 + - + +
107H GLU* 4.7 7.6 - - - +
108H ALA* 4.0 14.4 + - - +
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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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101H ILE* 3.3 40.9 + - + +
102H LYS 3.5 2.3 + - - +
104H LEU* 1.3 81.1 - - + +
106H ALA* 1.3 60.3 + - - +
107H GLU 3.3 0.4 - - - -
108H ALA* 3.2 8.5 + - + +
109H LYS* 2.8 50.4 + - + +
130H LEU* 5.1 3.1 - - + -
23I SER* 4.1 21.1 - - - +
24I SER* 5.6 0.2 - - - -
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Residues in contact with ALA 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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102H LYS 2.8 20.1 + - - +
103H ASN* 3.0 12.7 + - - +
105H LEU* 1.3 74.9 - - - +
107H GLU* 1.3 60.7 + - - +
109H LYS* 3.2 5.7 + - - +
110H LYS* 2.9 44.3 + - - +
127H VAL* 4.7 2.7 - - + +
130H LEU* 3.7 25.1 - - + -
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Residues in contact with GLU 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 ASN* 3.0 19.7 + - + +
104H LEU* 4.7 9.0 - - - +
106H ALA* 1.3 74.6 - - - +
108H ALA* 1.3 60.1 + - - +
110H LYS* 3.3 24.8 + - - +
111H ASN* 2.8 37.9 + - - +
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Residues in contact with ALA 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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104H LEU 4.0 11.0 + - - +
105H LEU* 3.2 15.7 + - + +
107H GLU* 1.3 78.9 - - - +
109H LYS* 1.3 62.8 + - + +
111H ASN* 3.2 13.4 + - - +
112H VAL* 2.9 34.2 + - + +
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Residues in contact with LYS 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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105H LEU* 2.8 39.5 + - + +
106H ALA* 3.5 11.4 - - - +
107H GLU 3.2 0.2 - - - -
108H ALA* 1.3 79.0 - - + +
110H LYS* 1.3 60.1 + - - +
112H VAL* 3.2 10.4 + - + +
113H SER* 2.9 22.9 + - - -
123H ALA* 3.3 24.5 - - + +
126H GLN* 2.8 46.7 + - + +
127H VAL* 4.4 7.6 - - + +
130H LEU* 5.3 7.5 - - + +
20I ALA* 5.7 1.2 - - - +
23I SER* 4.9 14.6 - - - -
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Residues in contact with LYS 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 ALA* 2.9 44.7 + - - +
107H GLU* 3.4 23.3 - - - +
109H LYS* 1.3 76.5 - - - +
111H ASN* 1.3 63.1 + - - +
113H SER* 2.3 31.0 + - - +
114H SER* 3.8 6.2 + - - -
127H VAL* 3.7 24.5 - - + -
131H GLU* 5.5 4.0 - - - +
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Residues in contact with ASN 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 GLU* 2.8 30.6 + - - +
108H ALA* 3.2 12.2 + - - +
110H LYS* 1.3 78.1 - - - +
112H VAL* 1.3 64.1 + - + +
114H SER* 3.3 17.5 + - - -
115H SER* 4.0 5.4 + - - -
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Residues in contact with VAL 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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108H ALA* 2.9 20.1 + - + +
109H LYS* 3.2 14.8 + - + +
111H ASN* 1.3 74.8 - - + +
113H SER* 1.3 56.6 + - - +
114H SER 3.1 1.8 - - - -
115H SER* 3.0 31.0 + - - +
119H GLU* 3.8 26.9 - - + +
120H ALA* 3.5 6.4 - - - -
123H ALA* 3.7 15.3 - - + -
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Residues in contact with SER 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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109H LYS 2.9 12.4 + - - -
110H LYS* 2.3 32.6 + - - +
112H VAL* 1.3 75.9 - - - +
114H SER* 1.3 58.3 + - - +
115H SER 3.4 0.7 - - - -
120H ALA* 3.3 23.3 - - - +
123H ALA* 3.6 14.3 - - - +
124H ALA* 4.6 9.2 - - - -
127H VAL* 5.3 2.2 - - - -
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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