Contacts of the helix formed by residues 100 - 113 (chain D) in PDB entry 6P7B
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D GLY 4.9 2.8 - - - +
97D SER* 2.3 36.4 + - - +
98D TYR 3.4 3.8 - - - -
99D ARG* 1.3 80.8 + - - +
101D ARG* 1.3 62.8 + - - +
102D LYS 3.5 1.6 - - - -
103D LYS* 4.0 28.9 + - + +
104D GLN* 2.9 33.9 + - - +
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Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D PHE* 4.8 9.8 - - + -
98D TYR* 2.6 56.2 + - - +
99D ARG* 3.6 2.0 - - - -
100D ASN* 1.3 80.4 - - - +
102D LYS* 1.3 70.0 + - + +
103D LYS 3.0 1.4 + - - -
104D GLN* 3.2 9.9 + - - +
105D SER* 3.0 32.9 + - - +
130D LEU* 3.9 28.1 - - - +
131D ASP* 3.4 39.9 + - - +
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Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ARG 5.4 3.7 + - - +
100D ASN 3.5 0.4 - - - -
101D ARG* 1.3 79.3 - - + +
103D LYS* 1.3 70.9 + - + +
105D SER* 4.6 3.4 - - - -
106D ILE* 2.9 32.4 + - + +
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ARG 4.9 6.7 + - - -
100D ASN* 4.0 28.2 + - + +
101D ARG 3.0 2.6 + - - -
102D LYS* 1.3 84.9 - - + +
104D GLN* 1.3 60.9 + - - +
106D ILE* 3.8 3.7 - - - +
107D ASP* 2.9 30.3 + - - +
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ASN* 2.9 39.6 + - - +
101D ARG* 3.4 9.8 - - - +
103D LYS* 1.3 81.3 - - - +
105D SER* 1.3 70.5 + - - +
107D ASP* 4.5 4.0 - - - -
108D VAL* 2.9 30.6 + - + +
138D ASN* 4.5 15.8 - - - +
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Residues in contact with SER 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ARG* 3.0 27.8 + - - +
102D LYS* 3.9 3.4 - - - -
104D GLN* 1.3 80.0 + - - +
106D ILE* 1.3 57.7 + - - +
109D PHE* 3.0 50.8 + - - -
134D ALA* 3.2 29.4 - - - +
138D ASN* 4.3 8.5 + - - +
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LYS* 2.9 31.3 + - + +
103D LYS* 3.8 4.7 - - - +
105D SER* 1.3 74.1 - - - +
107D ASP* 1.3 61.3 + - + +
109D PHE* 4.4 14.1 - - + -
110D ILE* 2.9 50.7 + - + +
124D LEU* 6.0 9.4 - - + -
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LYS 2.9 22.4 + - - +
104D GLN* 4.0 3.8 - - - +
106D ILE* 1.3 80.9 - - + +
108D VAL* 1.3 58.2 + - - +
110D ILE* 3.9 5.0 - - - +
111D GLN* 2.6 66.5 + - - +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLN* 2.9 17.9 + - + +
105D SER 4.2 0.2 - - - +
107D ASP* 1.3 77.3 - - - +
109D PHE* 1.3 71.9 + - + +
111D GLN* 4.5 6.1 - - + +
112D LYS* 2.9 29.4 + - + +
113D ILE 4.1 0.5 + - - -
137D PHE* 3.4 29.7 - - + -
138D ASN* 3.5 21.8 - - - +
141D LEU* 4.0 16.8 - - + -
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D SER* 3.0 37.1 + - - +
106D ILE* 3.8 15.3 - - + +
108D VAL* 1.3 83.6 - - + +
110D ILE* 1.3 65.4 + - - +
111D GLN 2.9 0.3 + - - -
113D ILE* 2.9 46.8 + - + +
120D LYS* 5.4 0.4 - - - +
124D LEU* 6.6 0.4 - - + -
133D ILE* 3.7 32.5 - - + -
134D ALA* 3.7 28.5 - - + -
137D PHE* 3.4 39.9 - + + -
138D ASN* 4.7 2.2 - - - -
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Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ILE* 2.9 39.8 + - + +
107D ASP* 4.1 6.5 - - - +
109D PHE* 1.3 73.1 - - - +
111D GLN* 1.3 68.4 + - + +
113D ILE* 5.0 0.4 - - - -
114D SER* 4.7 6.2 + - - -
120D LYS* 3.4 31.7 + - - +
124D LEU* 5.7 2.2 - - + -
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Residues in contact with GLN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP* 2.6 47.9 + - - +
108D VAL* 4.0 6.4 - - - +
109D PHE 2.9 0.2 + - - -
110D ILE* 1.3 87.3 - - + +
112D LYS* 1.3 68.7 + - + +
113D ILE 3.8 0.4 - - - -
114D SER* 5.0 2.7 + - - -
115D GLU* 2.8 21.3 - - - +
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D VAL* 2.9 19.8 + - - +
111D GLN* 1.3 85.0 - - + +
113D ILE* 1.3 64.4 + - - +
114D SER 3.4 0.9 - - - -
115D GLU* 3.0 19.4 - - - +
116D TYR* 3.2 45.6 - - + +
137D PHE* 4.8 2.1 - - + -
141D LEU* 3.7 27.1 - - + +
145D GLU* 3.3 28.3 + - - +
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 5.0 7.9 - - + +
109D PHE* 2.9 39.7 + - + +
111D GLN 3.8 0.2 - - - -
112D LYS* 1.3 78.8 - - - +
114D SER* 1.3 67.2 + - - +
115D GLU 3.3 0.9 + - - -
116D TYR* 3.4 10.8 + - - +
117D THR* 3.2 24.3 + - + +
120D LYS* 3.4 48.2 - - + +
124D LEU* 5.1 6.5 - - + -
137D PHE* 3.8 30.3 - - + -
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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