Contacts of the helix formed by residues 80 - 94 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.5 4.0 - - - -
41C GLU* 2.8 22.7 - - - +
77C GLU 4.3 11.0 - - - +
78C GLU 3.6 7.0 + - - +
79C VAL* 1.3 78.7 - - - +
81C VAL* 1.3 53.5 + - - +
82C LYS* 4.1 6.4 + - - +
83C GLY* 3.1 17.1 + - - -
84C PHE* 2.8 34.8 + - - +
105C GLU* 4.0 13.7 + - - +
109C CYS* 5.4 1.2 - - - +
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.5 31.9 - - + +
41C GLU* 3.3 25.4 + - + +
43C GLN* 3.5 15.0 - - + -
45C PHE* 3.7 24.2 - - + -
80C THR* 1.3 72.1 - - - +
82C LYS* 1.3 57.3 + - - +
84C PHE* 4.4 2.2 - - - -
85C GLU* 2.9 46.8 + - - +
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Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C THR* 3.3 6.6 - - - +
81C VAL* 1.3 79.2 - - - +
83C GLY* 1.3 57.8 + - - +
85C GLU* 5.3 1.6 - - - -
86C PRO* 3.3 22.2 - - - +
101C GLU* 5.9 3.6 - - + +
102C ASN* 3.9 16.3 + - + +
105C GLU* 4.5 9.6 - - + -
106C VAL* 3.9 5.7 - - - +
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Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C THR* 3.1 14.1 + - - -
82C LYS* 1.3 78.3 - - - +
84C PHE* 1.3 63.9 + - - +
85C GLU 3.6 0.2 - - - -
86C PRO* 3.5 6.8 - - - +
87C LEU* 3.5 21.1 - - - +
105C GLU* 3.5 29.8 - - - +
106C VAL* 3.8 7.5 - - - +
109C CYS* 4.1 7.6 - - - -
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.1 20.0 - - + -
40C VAL* 3.7 16.8 - - + -
45C PHE* 3.7 36.1 - + + -
52C LEU* 5.6 4.7 - - + -
59C PHE* 4.0 16.8 - + - -
75C LEU* 3.8 26.9 - - + -
79C VAL* 3.9 8.7 - - + -
80C THR 2.8 19.4 + - - +
81C VAL* 4.0 2.2 - - - +
83C GLY* 1.3 74.2 - - - +
85C GLU* 1.3 62.0 + - - +
87C LEU* 2.8 22.7 + - + +
88C ILE* 3.0 38.8 + - + -
109C CYS* 4.0 5.8 - - - -
113C LEU* 4.0 14.8 - - + -
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Residues in contact with GLU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 4.1 25.3 - - + -
81C VAL* 2.9 26.3 + - - +
82C LYS* 5.3 1.3 - - - -
84C PHE* 1.3 81.1 - - - +
86C PRO* 1.4 64.4 - - + +
88C ILE* 3.4 3.4 + - - +
89C GLN* 3.0 39.4 + - + +
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Residues in contact with PRO 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LYS* 3.3 26.0 - - - +
83C GLY 3.5 4.0 - - - +
84C PHE 3.3 4.5 - - - -
85C GLU* 1.4 96.6 - - + +
87C LEU* 1.3 55.1 + - - +
89C GLN* 3.5 8.9 - - + +
90C PHE* 2.9 26.0 + - - +
95C LYS 4.5 1.9 - - - +
96C LEU* 4.0 16.0 - - + +
97C ILE* 4.2 18.1 + - + +
102C ASN* 4.0 11.4 - - - +
106C VAL* 3.9 14.6 - - + -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLY 3.5 19.5 - - - +
84C PHE* 2.8 9.8 + - + +
86C PRO* 1.3 75.3 - - - +
88C ILE* 1.3 60.8 + - - +
89C GLN 3.2 0.7 - - - -
90C PHE* 3.3 5.5 + - + +
91C ALA* 2.9 28.4 + - - +
96C LEU* 4.0 6.3 - - + -
106C VAL* 3.8 14.8 - - + +
109C CYS* 3.6 25.8 - - + +
110C VAL* 3.4 42.6 - - + +
113C LEU* 4.1 11.2 - - + -
115C VAL* 4.3 13.7 - - + +
118C ILE* 3.7 20.4 - - + -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 5.0 7.2 - - + -
52C LEU* 5.8 5.8 - - + -
84C PHE* 3.0 39.7 + - + -
85C GLU* 3.9 7.4 - - - +
87C LEU* 1.3 74.6 - - - +
89C GLN* 1.3 63.0 + - - +
91C ALA* 3.3 6.5 + - - +
92C TYR* 3.2 34.8 + - + +
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN* 5.8 0.7 - - - -
85C GLU* 3.0 30.2 + - + +
86C PRO* 3.5 8.7 - - + +
88C ILE* 1.3 76.9 - - - +
90C PHE* 1.3 51.2 + - - +
92C TYR* 3.1 3.5 + - - -
93C THR* 2.7 51.3 + - + +
95C LYS 4.2 3.1 - - - +
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Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C PRO 2.9 18.1 + - - +
87C LEU* 3.3 9.2 + - + +
89C GLN* 1.3 74.4 - - - +
91C ALA* 1.3 68.1 + - - +
93C THR* 4.2 0.7 - - - -
94C ALA* 2.8 56.4 + - - -
95C LYS 3.4 19.0 + - - +
96C LEU* 3.8 15.3 - - + -
115C VAL* 4.8 7.2 - - + -
116C HIS 4.1 7.2 - - - -
117C ASN 3.6 18.8 - - - -
118C ILE* 3.7 28.5 - - + -
11D TYR* 4.4 11.9 - + - -
13D SER* 4.2 7.6 - - - -
16D HIS* 3.2 36.6 + + + -
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 3.8 9.7 - - - +
51C VAL* 4.3 5.4 - - + +
52C LEU* 5.5 5.8 - - + -
55C CYS* 3.6 31.0 - - + -
87C LEU 2.9 13.5 + - - +
88C ILE* 3.3 13.9 + - - +
90C PHE* 1.3 78.0 - - - +
92C TYR* 1.3 69.8 + - + +
115C VAL* 6.2 1.8 - - + -
16D HIS* 2.7 25.7 + - - -
20D VAL* 4.3 0.2 - - - +
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 3.2 26.6 - - + +
22C LEU* 4.8 1.0 + - - -
24C LEU* 3.7 18.6 - - + -
25C ASN* 3.2 51.5 - - - +
28C ARG* 4.2 11.2 - - + -
46C ARG 5.6 0.4 - - - -
47C ALA* 3.7 6.8 - - + +
48C HIS* 2.9 52.7 + + - +
51C VAL* 3.7 23.6 - - + +
52C LEU* 4.4 16.6 - - + -
88C ILE* 3.2 23.8 + - + +
89C GLN* 3.1 4.7 + - - +
90C PHE 3.0 0.6 - - - -
91C ALA* 1.3 83.8 - - + +
93C THR* 1.3 59.9 + - + +
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1B SER* 4.1 20.7 + - - +
0B MET* 5.6 5.5 - - - +
21C LEU* 3.8 6.6 - - - +
25C ASN* 3.6 24.5 - - - +
89C GLN* 2.7 33.5 + - + +
92C TYR* 1.3 80.3 - - + +
94C ALA* 1.3 65.5 + - - +
95C LYS* 3.2 23.3 + - - +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B MET* 6.4 1.3 - - + -
21C LEU* 4.4 3.8 - - + -
90C PHE* 2.8 33.9 + - - -
93C THR* 1.3 73.5 - - - +
95C LYS* 1.3 57.1 + - - +
12D GLU* 3.4 3.3 - - - +
13D SER 2.9 48.3 + - - +
16D HIS* 3.5 27.1 - - + -
17D SER* 4.8 4.7 - - - +
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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