Contacts of the helix formed by residues 66 - 79 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.7 24.4 - - - +
63A GLN 2.9 18.6 + - - -
64A SER 2.9 0.9 - - - -
65A ALA* 1.3 78.7 - - - +
67A LYS* 1.3 67.2 + - - +
68A PRO 3.3 1.1 - - - -
69A PHE* 3.0 20.9 + - - +
70A THR* 3.2 13.8 + - - +
142A MET* 3.8 13.4 - - - +
194A GLN* 2.9 30.1 + - - +
195A CYS* 4.1 5.0 - - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 2.9 37.8 + - - +
66A SER* 1.3 82.1 + - - +
68A PRO* 1.3 63.7 - - + +
70A THR* 3.2 7.7 + - - -
71A TYR* 3.1 24.9 + - - +
94A GLU* 4.3 2.0 + - - -
111A ALA* 3.7 14.7 - - - +
112A MET* 2.9 40.5 + - + +
113A ILE* 4.0 0.4 - - - +
114A ASN* 2.7 30.5 + - - +
117A ALA* 3.6 26.0 - - + -
120A VAL* 5.1 0.7 - - - +
191A TYR* 2.9 26.5 - - + -
194A GLN* 4.4 0.7 - - - +
243A TYR* 4.5 3.2 + - - -
258A LYS* 4.9 0.2 - - - -
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Residues in contact with PRO 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 4.0 0.7 - - - +
65A ALA* 3.6 17.7 - - - +
66A SER 3.5 2.5 - - - -
67A LYS* 1.3 95.3 - - + +
69A PHE* 1.3 62.3 + - + +
71A TYR* 3.6 4.9 - - + +
72A ALA* 3.0 25.1 + - - +
112A MET* 3.8 16.6 - - + -
211A LEU* 4.9 2.9 - - + +
233A VAL* 3.4 32.5 - - + +
237A MET* 4.1 17.9 - - + -
258A LYS* 4.8 0.9 - - + -
266A LEU* 3.9 21.3 - - + -
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Residues in contact with PHE 69 (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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62A ILE* 4.2 3.6 - - + -
65A ALA 3.2 26.5 - - - -
66A SER* 3.0 11.1 + - - +
68A PRO* 1.3 78.3 - - + +
70A THR* 1.3 61.9 + - - +
71A TYR 3.2 0.2 - - - -
72A ALA* 3.2 7.3 - - + +
73A ALA 2.9 22.7 + - - -
141A ILE* 3.6 17.5 - - + +
142A MET* 3.8 20.0 - - + -
145A LEU* 3.4 31.9 - - + -
204A LEU* 5.0 0.2 - - + -
207A MET* 3.5 52.5 - - + -
211A LEU* 4.0 16.8 - - + -
266A LEU* 3.8 27.6 - - + -
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.2 6.9 + - - +
67A LYS* 3.2 11.3 + - - -
69A PHE* 1.3 74.2 - - + +
71A TYR* 1.3 61.8 + - - +
73A ALA* 3.2 7.2 + - - +
74A ALA* 2.8 32.1 + - - +
117A ALA* 5.6 1.9 + - - +
120A VAL* 3.5 15.6 - - - +
121A HIS 5.4 0.2 - - - -
124A LEU* 3.6 12.1 - - + +
138A ALA* 3.8 24.9 - - + +
141A ILE* 4.6 2.0 - - + -
142A MET* 5.7 2.5 - - - -
194A GLN* 3.3 44.6 + - + +
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Residues in contact with TYR 71 (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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67A LYS 3.1 20.3 + - - +
68A PRO* 3.6 6.3 - - + +
70A THR* 1.3 77.1 + - - +
72A ALA* 1.3 63.2 + - - +
74A ALA* 3.3 1.0 + - - +
75A LEU* 3.0 32.0 + - + +
83A VAL* 3.8 25.4 - - + -
84A ASP* 4.7 1.0 + - - -
87A VAL* 4.7 5.9 + - + +
88A GLY 4.5 3.6 + - - -
89A LEU* 3.5 15.2 - - - +
111A ALA* 3.7 32.5 - - + -
112A MET* 5.8 1.1 - - - -
120A VAL* 3.6 18.3 - - + +
232A ARG* 3.1 34.7 + - + +
233A VAL* 4.0 21.8 - - + -
236A VAL* 3.9 24.5 - - + +
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Residues in contact with ALA 72 (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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68A PRO 3.0 17.2 + - - +
69A PHE* 3.2 13.5 - - + +
71A TYR* 1.3 77.9 - - - +
73A ALA* 1.3 62.4 + - - +
75A LEU* 3.1 5.4 + - - +
76A VAL* 3.1 28.1 + - - +
141A ILE* 5.0 1.8 - - + -
211A LEU* 5.4 2.0 - - + -
225A LEU* 4.3 22.0 - - + -
229A VAL* 3.8 11.8 - - + +
233A VAL* 3.8 18.2 - - + -
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Residues in contact with ALA 73 (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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69A PHE 2.9 14.0 + - - +
70A THR 3.6 6.1 - - - +
72A ALA* 1.3 75.1 - - - +
74A ALA* 1.3 57.8 + - - +
76A VAL* 3.2 4.2 + - - +
77A ASP* 2.9 36.1 + - - +
124A LEU* 3.9 11.7 - - + -
137A ARG* 3.7 32.5 - - - +
141A ILE* 3.9 21.2 - - + +
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Residues in contact with ALA 74 (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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70A THR 2.8 21.2 + - - +
71A TYR* 3.6 4.9 - - - +
73A ALA* 1.3 71.4 - - - +
75A LEU* 1.3 57.4 + - - +
77A ASP* 4.5 4.9 - - - -
78A ARG* 2.9 34.5 + - - +
83A VAL* 3.6 16.1 - - + +
120A VAL* 4.0 25.4 - - + +
123A LEU* 4.4 13.0 - - + +
124A LEU* 4.0 7.1 - - + +
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Residues in contact with LEU 75 (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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71A TYR* 3.0 46.3 + - + +
72A ALA 3.1 6.7 + - - +
74A ALA* 1.3 76.9 - - - +
76A VAL* 1.3 58.2 + - - +
79A GLY* 2.9 28.1 + - - +
80A PHE* 3.7 50.1 + - + +
83A VAL* 3.9 18.2 - - + -
229A VAL* 4.2 26.2 - - + +
232A ARG* 3.9 27.6 - - + +
233A VAL* 4.5 2.0 - - + -
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Residues in contact with VAL 76 (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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72A ALA 3.1 15.4 + - - +
73A ALA* 3.6 7.0 - - - +
75A LEU* 1.3 79.2 - - - +
77A ASP* 1.3 60.4 + - - +
79A GLY* 4.5 1.6 + - - -
137A ARG* 4.3 14.4 - - - +
225A LEU* 4.0 23.6 - - + -
226A PRO* 4.0 23.8 - - + -
229A VAL* 4.0 11.2 - - + -
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Residues in contact with ASP 77 (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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73A ALA 2.9 18.0 + - - +
74A ALA 3.9 2.5 - - - +
76A VAL* 1.3 81.5 - - - +
78A ARG* 1.3 71.5 + - + +
124A LEU 2.4 31.9 - - - +
125A VAL* 4.1 13.3 - - - +
137A ARG* 2.9 37.1 + - - -
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Residues in contact with ARG 78 (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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74A ALA 2.9 16.4 + - - +
77A ASP* 1.3 83.6 - - + +
79A GLY* 1.3 64.2 + - - +
82A ALA* 3.6 34.5 + - + +
83A VAL* 4.3 3.8 - - + -
122A GLN 5.3 0.8 + - - -
123A LEU* 2.9 53.1 + - + +
125A VAL 4.0 4.5 - - - -
126A GLY* 3.3 23.7 - - - -
127A PRO* 3.4 35.8 - - - +
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Residues in contact with GLY 79 (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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75A LEU 2.9 22.5 + - - -
76A VAL 4.5 1.3 - - - -
77A ASP 3.7 1.2 - - - -
78A ARG* 1.3 82.7 - - - +
80A PHE* 1.3 65.4 + - - -
81A ALA 3.5 2.2 - - - -
82A ALA 3.7 0.3 + - - -
83A VAL* 3.4 21.6 + - - +
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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