Contacts of the helix formed by residues 97 - 113 (chain A) in PDB entry 2IHD
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 SER 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A THR* 3.3 7.1 - - - +
96A ARG* 1.3 77.7 - - - +
98A THR* 1.3 58.9 + - - +
99A ALA* 3.4 9.2 + - - +
100A LYS* 3.3 29.9 + - - +
101A LEU* 2.9 25.0 + - - +
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Residues in contact with THR 98 (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 ARG 4.2 7.4 - - - +
97A SER* 1.3 71.8 + - - +
99A ALA* 1.3 65.6 + - - +
101A LEU* 3.4 14.1 + - + +
102A VAL* 3.1 29.7 + - - +
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Residues in contact with ALA 99 (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 SER* 3.3 7.7 + - - +
98A THR* 1.3 81.6 + - - +
100A LYS* 1.3 62.2 + - - +
102A VAL* 3.4 6.7 + - - +
103A SER* 3.2 22.3 + - - -
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Residues in contact with LYS 100 (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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94A LYS 6.0 0.2 - - - -
95A THR* 4.0 21.5 + - + +
96A ARG 5.6 0.6 - - - +
97A SER* 3.3 23.2 + - - +
99A ALA* 1.3 74.9 - - - +
101A LEU* 1.3 67.9 + - - +
103A SER* 3.2 9.4 + - - +
104A LYS* 2.8 62.4 + - + +
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Residues in contact with LEU 101 (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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92A PHE* 3.4 27.4 - - + -
95A THR* 3.5 12.5 - - + +
96A ARG 5.7 2.0 - - - +
97A SER 2.9 17.9 + - - +
98A THR* 3.4 17.3 - - + +
99A ALA 3.3 0.2 - - - -
100A LYS* 1.3 75.9 - - - +
102A VAL* 1.3 59.4 + - + +
104A LYS* 4.9 0.2 - - - -
105A ALA* 2.9 26.7 + - - +
138A PRO* 3.6 35.9 - - + +
139A SER* 3.9 4.9 - - - +
140A LEU* 4.0 35.9 - - + +
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Residues in contact with VAL 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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98A THR* 3.1 17.4 + - - +
99A ALA* 3.8 6.3 - - - +
100A LYS 3.2 0.2 - - - -
101A LEU* 1.3 81.3 - - + +
103A SER* 1.3 63.1 + - - +
105A ALA* 3.3 2.3 + - - +
106A HIS* 3.2 45.6 + - + +
138A PRO* 4.2 27.4 - - + +
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Residues in contact with SER 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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99A ALA 3.2 12.1 + - - -
100A LYS* 3.2 14.0 + - - +
102A VAL* 1.3 80.2 - - - +
104A LYS* 1.3 65.0 + - - +
106A HIS* 3.3 7.5 + - - +
107A ARG* 3.1 31.0 + - - +
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Residues in contact with LYS 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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88A ALA 5.5 0.2 - - - +
91A GLU* 5.1 12.5 - - + +
92A PHE* 4.2 22.2 - - + +
95A THR* 4.2 12.3 - - - +
100A LYS* 2.8 57.3 + - + +
101A LEU* 4.1 2.5 - - - +
103A SER* 1.3 73.7 + - - +
105A ALA* 1.3 62.5 + - - +
107A ARG* 3.2 18.5 + - + +
108A ILE* 3.0 40.2 + - + +
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Residues in contact with ALA 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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92A PHE* 3.8 21.5 - - + -
101A LEU 2.9 19.1 + - - +
102A VAL 3.7 4.3 - - - +
103A SER 3.3 0.2 - - - -
104A LYS* 1.3 77.4 - - - +
106A HIS* 1.3 57.2 + - - +
109A PHE* 2.9 32.1 + - - +
135A LEU* 3.7 18.6 - - + -
138A PRO* 4.1 13.0 - - + -
142A CYS* 4.7 2.0 - - - -
143A PHE* 3.4 14.4 - - + -
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Residues in contact with HIS 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 VAL* 3.2 40.5 + - + +
103A SER* 3.7 8.5 - - - +
105A ALA* 1.3 76.2 - - - +
107A ARG* 1.3 57.8 + - + +
109A PHE* 3.8 1.7 - - - +
110A GLU* 3.0 50.3 + - - +
135A LEU* 3.6 45.9 + - + +
136A GLN* 6.0 1.3 - - - -
138A PRO* 4.6 2.2 - - + +
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Residues in contact with ARG 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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103A SER* 3.1 20.0 + - - +
104A LYS* 3.2 21.0 + - + +
106A HIS* 1.3 75.7 - - + +
108A ILE* 1.3 59.6 + - + +
110A GLU* 3.4 5.9 + - - +
111A GLU* 3.0 31.3 + - - +
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Residues in contact with ILE 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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85A PHE* 3.8 24.7 - - + -
88A ALA* 3.7 36.6 - - + +
89A CYS* 4.7 1.8 - - - +
92A PHE* 3.8 23.1 - - + -
104A LYS* 3.0 34.6 + - + +
107A ARG* 1.3 73.9 - - + +
109A PHE* 1.3 67.0 + - - +
111A GLU* 3.2 1.8 + - - -
112A PHE* 3.1 36.9 + - + +
113A VAL* 4.4 0.3 - - - +
143A PHE* 3.8 20.0 - - + -
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Residues in contact with PHE 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 ALA 2.9 18.8 + - - +
106A HIS 3.8 2.7 - - - +
108A ILE* 1.3 77.2 - - - +
110A GLU* 1.3 63.2 + - + +
113A VAL* 2.9 40.1 + - + -
114A ASP* 2.9 63.2 + - + -
128A ARG 4.3 1.6 - - - -
131A THR* 3.9 13.7 - - + -
132A ARG* 3.7 56.3 - - + -
135A LEU* 3.5 27.6 - - + -
143A PHE* 3.8 9.6 - + + -
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Residues in contact with GLU 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 HIS* 3.0 37.7 + - - +
107A ARG* 3.8 4.9 - - - +
109A PHE* 1.3 85.1 - - + +
111A GLU* 1.3 61.9 + - - +
114A ASP* 4.3 15.2 - - + +
117A ALA* 3.4 19.4 - - - +
118A PRO* 3.6 5.1 - - - +
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Residues in contact with GLU 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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107A ARG 3.0 17.6 + - - +
108A ILE* 3.2 3.3 + - - +
110A GLU* 1.3 79.8 - - - +
112A PHE* 1.3 68.3 + - + +
117A ALA* 3.2 5.4 - - - +
118A PRO* 3.5 23.4 - - - +
119A ARG* 2.8 81.5 + - - +
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Residues in contact with PHE 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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81A GLU* 4.0 4.5 - - - -
84A GLU* 3.8 9.0 - - + -
85A PHE* 3.6 63.0 - + + -
88A ALA* 4.1 15.3 - - + -
108A ILE* 3.1 26.5 + - + +
111A GLU* 1.3 87.9 - - + +
113A VAL* 1.3 60.1 + - + +
117A ALA* 3.6 5.8 - - - -
119A ARG* 3.3 66.9 - - + +
120A GLU* 3.3 3.8 - - - +
121A VAL* 2.9 32.6 + - + +
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Residues in contact with VAL 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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85A PHE* 3.8 33.2 - - + -
109A PHE* 2.9 43.0 + - + +
112A PHE* 1.3 84.0 - - + +
114A ASP* 1.3 69.7 + - - +
120A GLU* 5.0 4.8 - - - +
121A VAL* 5.0 4.7 - - + +
123A ILE* 4.4 10.7 - - + +
128A ARG* 3.2 39.9 - - + +
131A THR* 4.2 8.5 - - + -
143A PHE* 4.4 6.3 - - + -
146A ALA* 5.1 1.6 - - + -
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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