Contacts of the helix formed by residues 66 - 87 (chain C) in PDB entry 1AV1
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 PRO 66 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLU 4.6 1.1 - - - +
63C GLN* 2.9 22.2 - - - +
64C LEU* 3.8 11.4 - - + -
65C GLY* 1.4 85.6 - - - +
67C VAL* 1.3 56.9 + - - +
68C THR 3.6 0.2 - - - -
69C GLN* 3.1 29.2 - - + +
70C GLU* 2.9 32.6 + - - +
192D TYR* 4.2 6.6 - - + -
195D LYS* 4.3 22.7 - - + +
199D HIS* 5.6 2.0 - - + +
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TYR* 5.7 0.2 - - - +
67B VAL* 4.2 25.1 - - + -
71B PHE* 5.2 3.4 - - + -
72B TRP* 4.4 19.1 - - + -
64C LEU 3.0 17.7 + - - +
65C GLY* 2.7 11.0 + - - +
66C PRO* 1.3 76.3 - - - +
68C THR* 1.3 65.9 + - + +
70C GLU* 4.5 0.2 - - - +
71C PHE* 2.7 46.6 + - + +
72C TRP* 6.0 0.9 - - + -
192D TYR* 3.1 46.2 - - + +
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Residues in contact with THR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TRP* 6.0 3.1 - - + -
65C GLY* 3.5 13.5 - - - +
67C VAL* 1.3 83.8 - - + +
69C GLN* 1.3 68.4 - - + +
71C PHE* 4.8 0.4 - - - -
72C TRP* 3.0 47.5 - - - +
73C ASP* 3.0 11.8 + - - +
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY 4.3 1.8 - - - +
66C PRO* 3.1 37.5 - - + +
67C VAL 3.0 0.2 - - - -
68C THR* 1.3 87.4 - - + +
70C GLU* 1.3 70.0 + - + +
73C ASP* 3.4 23.1 + - - +
74C ASN* 4.0 2.6 + - - +
195D LYS* 3.9 11.0 + - - +
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Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PRO 2.9 14.0 + - - +
69C GLN* 1.3 87.6 - - + +
71C PHE* 1.3 66.1 + - + +
74C ASN* 2.8 40.3 + - - +
188D ARG* 5.3 1.2 - - - +
191D GLU* 4.1 31.1 - - + +
192D TYR* 4.3 7.5 + - + +
195D LYS* 3.1 44.7 + - + +
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Residues in contact with PHE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TYR* 3.8 28.9 - + - -
196A ALA* 5.6 2.5 - - + -
64B LEU* 5.5 4.9 - - + -
67B VAL* 5.4 3.1 - - + -
67C VAL* 2.7 28.5 + - + +
68C THR* 4.8 0.2 - - - -
70C GLU* 1.3 75.2 - - + +
72C TRP* 1.3 59.1 + + + +
74C ASN* 2.7 27.4 + - + +
75C LEU* 2.7 38.5 + - + +
188D ARG* 3.3 24.0 - - + -
189D LEU* 3.3 32.8 - - + -
192D TYR* 3.2 44.9 - + + -
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Residues in contact with TRP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 4.5 28.5 - - + +
64B LEU* 3.6 34.8 - - + -
65B GLY* 4.3 7.2 - - - -
67B VAL* 3.8 26.2 - - + -
68B THR* 4.8 7.2 - - - -
67C VAL* 6.0 0.9 - - + -
68C THR* 3.0 41.6 + - - +
71C PHE* 1.3 77.7 - + + +
73C ASP* 1.3 59.4 + - - +
75C LEU* 2.9 21.8 + - + +
76C GLU* 2.8 40.5 + - + +
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C THR* 3.0 20.4 + - - +
69C GLN* 3.4 16.1 + - - +
71C PHE 3.3 0.2 - - - -
72C TRP* 1.3 75.5 - - - +
74C ASN* 1.3 57.6 + - - +
76C GLU* 4.7 11.3 - - - +
77C LYS* 2.8 31.7 + - - +
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Residues in contact with ASN 74 (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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69C GLN 4.0 2.1 + - - +
70C GLU* 2.8 33.8 + - - +
71C PHE* 2.7 8.0 + - + +
73C ASP* 1.3 72.9 - - - +
75C LEU* 1.3 71.9 + - + +
77C LYS* 3.5 9.8 - - - +
78C GLU* 3.0 28.4 + - - +
188D ARG* 3.5 45.5 + - + +
191D GLU* 4.4 6.3 + - - -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 6.2 3.8 - - + -
64B LEU* 3.9 28.0 - - + -
71C PHE* 2.7 44.1 + - + +
72C TRP* 2.9 28.0 + - + +
74C ASN* 1.3 75.5 - - + +
76C GLU* 1.3 53.3 + - - +
77C LYS 2.9 2.7 - - - -
78C GLU* 2.6 12.8 + - - +
79C THR* 2.6 42.6 + - - +
185D GLY* 6.4 1.3 - - - -
188D ARG* 6.1 3.1 - - + -
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TRP* 2.8 26.1 + - + +
73C ASP* 4.8 10.5 - - - +
75C LEU* 1.3 73.2 - - - +
77C LYS* 1.3 64.0 + - - +
79C THR* 3.8 9.8 + - + -
80C GLU* 3.2 44.3 + - + +
81C GLY 3.8 0.9 + - - -
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Residues in contact with LYS 77 (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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73C ASP 2.8 23.5 + - - +
74C ASN* 3.5 13.5 - - - +
75C LEU 2.7 4.9 + - - -
76C GLU* 1.3 79.3 + - - +
78C GLU* 1.3 59.0 + - + +
81C GLY* 3.2 19.6 - - - +
188D ARG* 5.6 5.6 - - - +
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Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASN 3.0 15.4 + - - +
75C LEU* 2.6 10.1 + - - +
77C LYS* 1.3 76.8 - - + +
79C THR* 1.3 56.1 + - - +
81C GLY* 4.4 0.9 - - - -
82C LEU* 2.7 51.4 + - + +
181D LEU* 4.6 12.4 - - + +
184D ASN* 2.7 34.5 + - - +
185D GLY* 5.2 1.9 - - - -
188D ARG* 3.4 42.9 + - - +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 3.6 49.1 - - + +
58B SER* 4.1 5.2 - - - +
61B ARG* 5.6 6.1 - - + +
75C LEU* 2.6 33.6 + - - +
76C GLU* 3.8 6.9 + - + -
78C GLU* 1.3 76.3 - - - +
80C GLU* 1.3 60.9 + - + +
82C LEU* 3.1 0.7 + - - -
83C ARG* 2.9 21.9 + - - +
181D LEU* 4.6 17.8 - - + +
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Residues in contact with GLU 80 (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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58B SER* 6.0 0.9 - - - -
76C GLU* 3.2 33.3 + - + +
79C THR* 1.3 82.0 - - + +
81C GLY* 1.3 56.7 + - - +
83C ARG* 3.3 36.5 + - - +
84C GLN* 2.8 32.6 + - + +
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Residues in contact with GLY 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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76C GLU 3.8 1.0 + - - -
77C LYS 3.2 24.7 + - - -
78C GLU* 3.2 2.6 + - - -
79C THR 3.0 1.8 - - - -
80C GLU* 1.3 79.0 - - - +
82C LEU* 1.3 63.3 + - - +
84C GLN* 4.1 9.0 + - - +
85C GLU* 3.9 14.9 + - - +
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Residues in contact with LEU 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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57B PHE* 4.6 12.6 - - + -
78C GLU* 2.7 35.7 + - + +
79C THR 3.9 2.2 - - - +
81C GLY* 1.3 75.7 - - - +
83C ARG* 1.3 60.8 + - - +
84C GLN 3.1 1.8 - - - -
85C GLU* 3.2 25.7 + - + +
86C MET* 2.9 32.9 + - - +
177D ARG* 4.9 25.8 - - + +
180D ALA* 5.5 3.1 - - + -
181D LEU* 4.2 25.4 - - + +
184D ASN* 5.1 6.7 - - - +
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Residues in contact with ARG 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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50B TRP* 4.2 24.0 - - - -
53B VAL* 3.4 25.5 - - + +
54B THR* 3.3 31.0 - - - +
57B PHE* 4.1 27.8 - - + -
58B SER* 4.2 20.4 - - - +
79C THR 2.9 14.1 + - - +
80C GLU* 3.3 39.4 + - + +
82C LEU* 1.3 79.0 - - - +
84C GLN* 1.3 56.1 + - - +
86C MET* 3.9 2.4 - - - +
87C SER* 3.1 26.8 + - - -
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Residues in contact with GLN 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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80C GLU* 2.8 14.3 + - + +
81C GLY* 4.2 9.2 + - - +
82C LEU 3.1 0.2 - - - -
83C ARG* 1.3 77.3 - - - +
85C GLU* 1.3 64.9 + - - +
86C MET 3.2 0.4 - - - -
87C SER* 3.2 8.8 + - - +
88C LYS* 3.1 27.6 + - + +
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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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81C GLY 3.9 8.1 + - - +
82C LEU* 3.2 27.3 + - - +
84C GLN* 1.3 79.4 - - - +
86C MET* 1.3 52.8 + - - +
88C LYS* 3.6 4.5 - - - +
89C ASP* 2.7 35.3 + - - +
177D ARG* 3.4 31.4 + - - +
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Residues in contact with MET 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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53B VAL* 5.8 4.9 - - + -
57B PHE* 4.3 20.0 - - + -
82C LEU 2.9 15.7 + - - +
83C ARG* 4.0 7.0 - - - +
85C GLU* 1.3 75.3 - - - +
87C SER* 1.3 57.5 + - - +
88C LYS 3.0 1.6 - - - -
89C ASP* 3.5 12.6 - - + +
90C LEU* 2.7 38.4 + - + +
170D LEU* 5.2 7.0 - - + +
173D ARG* 4.2 11.4 - - + -
174D LEU* 3.5 41.7 - - + +
177D ARG* 3.0 41.1 - - + -
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Residues in contact with SER 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TRP* 4.6 26.1 - - - -
53B VAL* 5.4 10.5 - - - +
83C ARG* 3.1 18.1 + - - -
84C GLN* 3.2 14.7 + - - +
86C MET* 1.3 76.7 - - - +
88C LYS* 1.3 60.7 + - - +
90C LEU* 3.8 16.7 - - - +
91C GLU* 3.3 27.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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