Contacts of the helix formed by residues 66 - 79 (chain B) in PDB entry 3IH9
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 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ILE* 3.6 12.5 - - - +
63B GLN 2.9 18.3 + - - -
64B SER* 2.9 1.4 - - - -
65B ALA* 1.3 78.3 - - - +
67B LYS* 1.3 66.2 + - - +
68B PRO 3.3 1.3 - - - -
69B PHE* 3.0 20.7 + - - +
70B THR* 3.2 12.8 + - - +
142B MET* 3.7 26.7 - - - -
194B GLN* 3.1 31.2 + - - +
195B CYS* 4.2 3.5 - - - -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 2.6 40.6 + - - +
66B SER* 1.3 79.2 + - - +
68B PRO* 1.3 66.3 - - + +
70B THR* 3.3 8.3 + - - -
71B TYR* 3.2 23.2 + - - +
111B ALA* 3.6 15.6 - - - +
112B MET* 3.0 41.3 + - + +
113B ILE* 3.9 2.4 - - - +
114B ASN* 2.7 28.0 + - - +
117B ALA* 3.4 25.6 - - + -
120B VAL* 5.2 0.5 - - - +
191B TYR* 3.0 24.9 + - + +
194B GLN* 4.8 0.2 - - - +
243B TYR* 4.4 3.8 + - - -
258B LYS* 4.6 1.6 - - - -
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Residues in contact with PRO 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER 4.1 1.8 - - - +
65B ALA* 3.6 11.9 - - - +
66B SER 3.5 3.4 - - - -
67B LYS* 1.3 95.8 - - + +
69B PHE* 1.3 61.9 + - + +
71B TYR* 3.6 1.5 - - + +
72B ALA* 3.0 26.2 + - - +
112B MET* 3.9 15.5 - - + -
211B LEU* 4.8 2.0 - - + -
233B VAL* 3.3 33.7 - - + +
237B MET* 4.1 18.8 - - + -
258B LYS* 4.8 3.6 - - + -
266B LEU* 3.8 27.8 - - + -
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 4.3 3.4 - - + -
65B ALA 3.4 26.7 - - - -
66B SER* 3.0 9.4 + - - +
68B PRO* 1.3 77.6 - - + +
70B THR* 1.3 59.7 + - - +
71B TYR 3.2 1.3 - - - -
72B ALA* 3.1 6.9 + - + +
73B ALA* 2.8 27.4 + - - +
141B ILE* 3.6 15.0 - - + +
142B MET* 3.9 21.8 - - + -
145B LEU* 3.4 30.5 - - + -
204B LEU* 5.2 0.4 - - + -
207B MET* 3.5 46.9 - - + -
211B LEU* 3.9 23.8 - - + -
266B LEU* 3.7 25.8 - - + -
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 3.2 7.2 + - - +
67B LYS* 3.3 12.6 + - - +
69B PHE* 1.3 77.4 - - + +
71B TYR* 1.3 59.3 + - - +
73B ALA* 3.2 7.8 + - - +
74B ALA* 2.8 31.5 + - - +
117B ALA* 5.4 2.4 + - - -
120B VAL* 3.6 17.0 - - - +
121B HIS 5.6 0.4 - - - -
124B LEU* 3.7 10.7 - - + +
138B ALA* 4.1 20.4 - - + +
141B ILE* 4.7 1.6 - - + -
142B MET* 5.5 1.8 - - - -
194B GLN* 3.1 48.8 + - + +
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS 3.2 16.7 + - - +
68B PRO 3.6 4.5 - - - +
69B PHE 3.2 0.2 - - - -
70B THR* 1.3 79.9 + - - +
72B ALA* 1.3 57.5 + - - +
74B ALA* 3.8 0.6 - - - +
75B LEU* 3.0 48.1 + - + +
83B VAL* 3.8 24.7 - - + -
84B ASP* 4.6 1.7 + - - -
87B VAL* 4.5 7.3 + - + +
88B GLY 4.5 4.7 + - - -
89B LEU* 3.5 14.7 - - - +
111B ALA* 3.8 29.8 - - + -
112B MET* 4.5 8.1 - - + -
120B VAL* 3.8 16.8 - - + -
232B ARG* 3.0 31.8 + - + -
233B VAL* 4.1 19.3 - - + -
236B VAL* 4.1 22.0 - - + -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO 3.0 18.8 + - - +
69B PHE* 3.4 9.9 - - + +
71B TYR* 1.3 74.7 - - - +
73B ALA* 1.3 64.8 + - - +
75B LEU 3.4 0.5 + - - -
76B VAL* 3.1 28.6 + - - +
141B ILE* 5.1 1.1 - - + -
145B LEU* 6.0 0.2 - - + -
211B LEU* 5.4 2.5 - - + -
225B LEU* 4.1 28.3 - - + -
229B VAL* 3.7 10.2 - - + +
233B VAL* 3.8 17.5 - - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE 2.8 14.4 + - - +
70B THR 3.5 7.4 - - - +
72B ALA* 1.3 77.2 - - - +
74B ALA* 1.3 57.6 + - - +
76B VAL* 3.2 3.0 + - - +
77B ASP* 2.8 35.5 + - - +
124B LEU* 3.7 14.8 - - + -
137B ARG* 3.6 25.5 + - + +
141B ILE* 3.9 24.2 - - + +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B THR 2.8 20.8 + - - +
71B TYR* 3.8 4.3 - - - +
73B ALA* 1.3 74.3 - - - +
75B LEU* 1.3 57.4 + - - +
77B ASP* 4.4 4.3 - - - +
78B ARG* 2.9 34.1 + - - +
83B VAL* 3.6 17.2 - - + +
120B VAL* 4.0 25.1 - - + +
123B LEU* 4.4 9.6 - - + -
124B LEU* 3.8 10.0 - - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 3.0 58.4 + - + +
72B ALA 3.8 3.8 - - - +
74B ALA* 1.3 75.1 - - - +
76B VAL* 1.3 58.6 + - - +
79B GLY* 2.8 28.1 + - - +
80B PHE* 4.1 34.8 + - + -
83B VAL* 3.9 28.0 - - + -
84B ASP* 4.9 0.4 - - - +
229B VAL* 4.2 21.1 - - + +
232B ARG* 4.3 16.8 - - + +
233B VAL* 4.2 12.3 - - + -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA 3.1 17.2 + - - +
73B ALA* 3.2 4.2 + - - +
75B LEU* 1.3 80.2 - - - +
77B ASP* 1.3 61.2 + - - +
78B ARG 3.6 0.2 + - - -
79B GLY* 4.4 2.1 + - - -
137B ARG* 4.2 14.1 - - - +
225B LEU* 4.4 9.0 - - + -
226B PRO* 3.6 34.5 - - + -
229B VAL* 3.7 14.1 - - + -
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA 2.8 14.6 + - - +
74B ALA 4.0 2.5 - - - +
76B VAL* 1.3 80.7 - - - +
78B ARG* 1.3 68.1 + - + +
124B LEU 2.6 29.1 - - - +
125B VAL* 4.3 15.6 - - - +
137B ARG* 2.6 43.1 + - - -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA 2.9 13.4 + - - +
77B ASP* 1.3 85.2 - - + +
79B GLY* 1.3 66.2 + - - +
82B ALA* 3.7 36.1 + - + +
83B VAL* 4.2 4.0 - - + -
122B GLN* 4.7 2.4 + - - +
123B LEU* 3.0 59.1 + - + +
125B VAL 4.3 2.7 - - - -
126B GLY* 3.3 25.6 + - - -
127B PRO* 3.4 34.8 - - - +
134B ARG* 5.1 0.2 - - - +
181B GLN* 5.5 4.4 + - - -
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU 2.8 22.4 + - - -
76B VAL 4.4 2.3 + - - -
77B ASP 3.9 0.4 - - - -
78B ARG* 1.3 83.6 - - - +
80B PHE* 1.3 69.2 + - - +
81B ALA* 3.4 2.5 - - - -
82B ALA 3.3 6.5 + - - -
83B VAL* 3.4 10.2 + - - +
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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