Contacts of the helix formed by residues 80 - 94 (chain A) in PDB entry 2IHC
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 THR 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.7 4.3 - - - -
41A GLU* 3.7 21.1 - - - +
77A GLU 4.5 7.6 - - - +
78A GLU 3.5 9.7 + - - +
79A VAL* 1.3 77.7 - - - +
81A VAL* 1.3 54.4 + - - +
82A LYS* 3.6 9.6 + - - +
83A GLY* 3.0 18.8 + - - -
84A PHE* 2.8 35.9 + - - +
105A GLU* 4.0 10.6 + - + +
109A CYS* 5.4 1.6 - - - +
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Residues in contact with VAL 81 (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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40A VAL* 3.5 30.4 - - + +
41A GLU* 3.0 25.0 + - + +
43A GLN* 3.2 31.6 - - + +
45A PHE* 4.2 16.8 - - + -
80A THR* 1.3 72.7 - - - +
82A LYS* 1.3 58.8 + - - +
84A PHE* 4.3 2.9 - - - -
85A GLU* 2.8 37.4 + - + +
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Residues in contact with LYS 82 (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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41A GLU* 4.6 0.6 + - - -
80A THR* 3.3 8.4 - - - +
81A VAL* 1.3 79.6 - - - +
83A GLY* 1.3 55.7 + - - +
85A GLU* 5.4 1.1 - - - -
86A PRO* 3.3 22.6 - - - +
101A GLU* 6.3 2.9 - - + -
102A ASN* 4.0 14.5 - - + +
105A GLU* 4.5 9.4 - - + -
106A VAL* 3.9 5.7 - - - +
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Residues in contact with GLY 83 (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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80A THR* 3.0 15.3 + - - -
82A LYS* 1.3 78.9 - - - +
84A PHE* 1.3 60.2 + - - +
86A PRO* 3.7 5.1 - - - +
87A LEU* 3.2 25.3 - - - +
105A GLU* 3.6 30.9 - - - +
106A VAL* 3.8 6.1 - - - +
109A CYS* 4.1 7.9 - - - -
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Residues in contact with PHE 84 (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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38A ILE* 4.0 15.7 - - + -
40A VAL* 3.7 25.6 - - + -
45A PHE* 4.0 28.9 - + + -
52A LEU* 5.7 0.9 - - + -
59A PHE* 3.9 11.7 - + - -
75A LEU* 3.7 19.3 - - + -
79A VAL* 4.1 4.3 - - + -
80A THR 2.8 19.9 + - - +
81A VAL* 4.0 2.2 - - - +
83A GLY* 1.3 73.6 - - - +
85A GLU* 1.3 66.8 + - - +
87A LEU* 2.9 15.5 + - + +
88A ILE* 3.0 48.1 + - + -
109A CYS* 4.0 4.9 - - - -
113A LEU* 3.6 29.4 - - + -
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Residues in contact with GLU 85 (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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28A ARG* 5.7 1.0 + - - -
45A PHE* 4.4 20.0 - - + -
81A VAL* 2.8 29.7 + - + +
82A LYS* 5.8 0.7 - - - -
84A PHE* 1.3 74.7 - - - +
86A PRO* 1.3 71.7 - - + +
88A ILE* 3.2 11.7 - - - +
89A GLN* 2.5 68.9 + - - +
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Residues in contact with PRO 86 (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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82A LYS 3.3 24.9 - - - +
83A GLY 3.7 2.7 - - - +
84A PHE 3.5 2.9 - - - -
85A GLU* 1.3 103.6 - - + +
87A LEU* 1.3 51.0 + - - +
89A GLN* 3.6 8.2 + - + +
90A PHE* 2.8 30.8 + - - +
95A LYS 4.3 2.4 - - - +
96A LEU* 3.5 23.8 - - + +
97A ILE* 4.2 11.3 + - + +
102A ASN* 4.1 12.3 - - - +
106A VAL* 3.9 14.4 - - + -
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Residues in contact with LEU 87 (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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83A GLY 3.2 20.0 - - - +
84A PHE* 2.9 11.3 + - + +
86A PRO* 1.3 73.8 - - - +
88A ILE* 1.3 62.2 + - - +
89A GLN 3.1 0.9 - - - -
90A PHE* 3.5 5.8 - - + +
91A ALA* 2.9 28.9 + - - +
96A LEU* 4.0 13.2 - - + -
106A VAL* 3.6 24.9 - - + +
109A CYS* 3.7 22.0 - - + +
110A VAL* 3.3 29.6 - - + +
113A LEU* 5.2 2.0 - - + -
115A VAL* 4.6 19.4 - - + +
118A ILE* 3.7 19.5 - - + -
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Residues in contact with ILE 88 (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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28A ARG* 4.1 23.9 - - - +
38A ILE* 5.2 2.2 - - + -
45A PHE* 4.3 21.3 - - + -
46A ARG 4.4 0.9 - - - +
47A ALA* 4.2 24.5 - - + -
52A LEU* 4.4 11.4 - - + -
84A PHE* 3.0 47.2 + - + +
85A GLU* 3.2 21.8 - - - +
87A LEU* 1.3 78.5 - - - +
89A GLN* 1.3 61.5 + - + +
91A ALA* 3.5 4.2 + - + +
92A TYR* 3.3 38.6 + - + +
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Residues in contact with GLN 89 (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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28A ARG* 3.4 27.5 + - - +
29A LYS* 5.6 2.6 - - - +
85A GLU* 2.5 50.6 + - - +
86A PRO* 3.6 7.1 - - + +
88A ILE* 1.3 77.5 - - + +
90A PHE* 1.3 56.3 + - - +
92A TYR* 3.3 1.8 + - - -
93A THR* 2.6 45.9 + - + +
95A LYS 4.2 2.5 - - - +
97A ILE* 6.3 0.8 - - - +
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Residues in contact with PHE 90 (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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86A PRO 2.8 21.7 + - - +
87A LEU* 3.3 9.4 + - + +
89A GLN* 1.3 73.0 - - - +
91A ALA* 1.3 64.7 + - - +
92A TYR 3.0 0.2 + - - -
93A THR* 4.0 0.4 - - - -
94A ALA* 2.7 56.1 + - - -
95A LYS 3.4 18.8 + - - +
96A LEU* 3.8 14.4 - - + -
115A VAL* 4.2 11.2 - - + -
116A HIS 3.6 12.6 - - - -
117A ASN 3.5 21.5 - - - -
118A ILE* 3.4 27.8 - - + -
11B TYR* 4.1 11.4 - + - -
13B SER* 3.9 11.7 - - - -
16B HIS* 3.4 24.9 + + - -
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Residues in contact with ALA 91 (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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21A LEU* 3.8 10.6 - - - +
51A VAL* 4.2 3.9 - - + +
52A LEU* 5.5 5.4 - - + -
55A CYS* 3.8 28.5 - - + -
87A LEU 2.9 17.0 + - - +
88A ILE* 3.6 10.8 - - + +
90A PHE* 1.3 80.4 - - + +
92A TYR* 1.3 67.3 + - + +
115A VAL* 5.9 1.8 - - + -
16B HIS* 2.9 27.3 + - - -
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Residues in contact with TYR 92 (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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21A LEU* 3.4 32.9 - - + +
22A LEU* 4.6 1.0 + - - +
24A LEU* 3.5 37.2 - - + -
25A ASN* 3.3 32.8 - - - +
28A ARG* 3.6 25.6 - - + +
47A ALA* 3.7 6.8 - - + +
48A HIS* 2.6 47.7 + + - +
51A VAL* 3.6 24.1 - - + +
52A LEU* 4.6 5.2 - - + -
88A ILE* 3.3 30.9 + - + +
89A GLN 3.3 3.9 + - - +
90A PHE 3.0 0.4 - - - -
91A ALA* 1.3 83.6 - - + +
93A THR* 1.3 59.3 + - - +
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Residues in contact with THR 93 (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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18A THR* 5.9 3.3 - - - +
21A LEU* 4.1 6.4 - - - +
22A LEU* 6.3 4.0 - - + -
25A ASN* 3.3 30.1 - - - +
28A ARG* 5.9 0.2 - - - +
89A GLN* 2.6 29.1 + - + +
92A TYR* 1.3 78.2 - - - +
94A ALA* 1.3 66.5 + - - +
95A LYS* 3.0 51.1 + - - +
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Residues in contact with ALA 94 (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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18A THR* 6.6 0.2 - - + -
21A LEU* 4.6 4.0 - - + -
90A PHE* 2.7 31.8 + - - -
92A TYR 4.0 0.4 - - - -
93A THR* 1.3 73.0 - - - +
95A LYS* 1.3 60.0 + - - +
12B GLU* 3.5 10.0 - - - +
13B SER 3.1 40.7 + - - +
16B HIS* 3.9 23.5 - - + -
17B SER* 5.1 5.8 - - - +
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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