Contacts of the helix formed by residues 67 - 87 (chain C) in PDB entry 3D87
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 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C SER 4.5 7.3 + - - -
11C TRP* 4.4 21.7 - - - -
63C LEU* 4.0 27.8 - - - -
65C ASP 3.7 3.0 + - - -
66C ASN* 1.3 75.1 - - - +
68C GLN* 1.3 62.9 + - - +
69C PHE 3.4 2.0 - - - -
70C CYS* 3.4 5.4 - - - +
71C LEU* 2.7 44.3 + - - +
168C LEU* 4.8 3.6 - - - -
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 3.3 26.0 - - + +
5C GLY* 3.1 36.3 - - - +
6C GLY 4.6 4.0 + - - +
7C SER* 3.5 24.5 - - - +
9C PRO* 5.4 0.3 - - - +
66C ASN* 3.6 3.7 - - - +
67C SER* 1.3 82.3 + - - +
69C PHE* 1.3 65.7 + - - +
71C LEU* 3.4 9.5 + - - +
72C GLN* 3.0 43.6 + - - +
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C VAL* 5.3 5.4 - - + -
4C PRO* 4.5 20.7 - - + +
55C GLY 4.3 5.4 - - - -
56C ASP* 3.3 49.4 - - + +
66C ASN* 3.7 18.9 + - - +
67C SER 3.4 0.4 - - - -
68C GLN* 1.3 75.8 - - - +
70C CYS* 1.3 64.2 + - - +
72C GLN* 3.0 13.6 + - + +
73C ARG* 2.9 43.7 + - + +
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Residues in contact with CYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 5.2 0.4 - - - -
56C ASP 3.0 17.1 + - - +
57C GLY 3.3 12.1 - - - +
58C CYS* 3.0 43.3 - - - -
63C LEU* 4.1 6.5 - - + -
66C ASN 5.7 0.2 - - - -
67C SER* 3.4 11.6 + - - +
69C PHE* 1.3 78.3 - - - +
71C LEU* 1.3 66.4 + - + +
73C ARG* 3.0 8.9 - - - +
74C ILE* 2.9 37.4 + - - +
160C VAL* 3.9 5.4 - - - -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PRO* 3.6 36.1 - - + -
11C TRP* 4.7 11.0 - - + -
63C LEU* 5.3 0.4 - - + -
67C SER* 2.7 30.6 + - - +
68C GLN* 4.0 13.5 - - - +
70C CYS* 1.3 75.2 - - + +
72C GLN* 1.3 53.4 + - - +
74C ILE* 3.3 25.2 - - + +
75C HIS* 2.7 37.6 + - - +
116C LEU* 4.0 10.5 - - + +
160C VAL* 3.8 16.6 - - + -
161C PHE* 3.8 21.8 - - + -
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Residues in contact with GLN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 3.3 31.4 - - - +
68C GLN* 3.0 28.4 + - - +
69C PHE* 3.0 17.4 + - + +
71C LEU* 1.3 75.8 - - - +
73C ARG* 1.3 53.2 - - - +
75C HIS* 3.7 8.0 - - - +
76C GLN* 2.9 33.1 + - - +
117C GLN* 4.3 18.2 - - - +
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Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PRO* 5.0 2.0 - - - -
51C HIS 3.7 15.6 + - - +
52C ILE* 3.7 20.6 - - + -
53C GLN* 3.0 21.3 - - - +
56C ASP* 2.3 52.0 + - + +
69C PHE* 2.9 33.9 + - + +
70C CYS* 3.0 14.4 - - - +
72C GLN* 1.3 72.2 - - - +
74C ILE* 1.3 57.6 + - - +
76C GLN* 2.4 65.8 + - - +
77C GLY 3.0 4.5 + - - -
153C PHE* 4.7 2.0 - - + -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 3.5 19.7 - - + -
70C CYS* 2.9 16.4 + - - +
71C LEU* 3.3 33.4 - - + +
73C ARG* 1.3 77.2 - - - +
75C HIS* 1.3 67.7 + - - +
77C GLY 2.9 12.6 + - - -
78C LEU* 3.1 15.5 - - + +
116C LEU* 3.4 21.8 - - + -
153C PHE* 2.9 19.8 - - + -
157C ALA* 4.2 11.2 - - + -
160C VAL* 3.6 25.4 - - + -
161C PHE* 3.9 16.6 - - + -
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Residues in contact with HIS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU 2.7 20.7 + - - +
72C GLN* 3.7 5.4 - - - +
74C ILE* 1.3 73.3 - - - +
76C GLN* 1.3 67.4 + - - +
78C LEU* 3.4 14.2 + - - +
79C ILE* 3.0 46.2 + - + +
113C SER* 3.5 24.5 + - - -
116C LEU* 3.5 12.6 - - + -
117C GLN* 3.4 55.2 + - + +
119C GLU 5.9 0.7 - - - -
120C GLY* 5.1 2.6 - - - -
121C HIS 5.5 1.2 + - - -
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PRO* 3.9 24.0 - - + +
72C GLN 2.9 13.7 + - - +
73C ARG* 2.4 57.3 + - - +
75C HIS* 1.3 79.4 - - + +
77C GLY* 1.3 59.0 + - - +
79C ILE* 3.4 7.1 + - - +
80C PHE* 3.0 19.2 + - - +
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PRO* 4.0 15.9 - - - -
73C ARG 3.0 5.1 + - - -
74C ILE 2.9 4.8 + - - -
76C GLN* 1.3 73.1 - - - +
78C LEU* 1.3 52.6 - - - +
80C PHE* 2.6 8.0 + - - +
81C TYR* 2.6 44.4 + - - -
153C PHE* 3.4 24.2 - - - -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 5.1 3.6 - - + -
74C ILE* 3.1 15.9 + - + +
75C HIS* 3.4 19.5 - - - +
77C GLY* 1.3 72.5 - - - +
79C ILE* 1.3 52.9 + - - +
81C TYR* 4.7 3.8 - - + -
82C GLU* 2.5 45.7 + - - +
109C LEU* 4.2 28.7 - - + +
112C LEU* 4.2 11.7 - - + -
113C SER* 3.6 38.8 - - - +
116C LEU* 3.8 11.4 - - + -
153C PHE* 3.6 19.7 - - + -
154C VAL* 5.2 2.7 - - + -
157C ALA* 5.8 2.5 - - + -
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C HIS* 3.0 33.9 + - + +
76C GLN* 3.5 11.7 - - - +
78C LEU* 1.3 74.9 - - - +
80C PHE* 1.3 56.3 + - - +
82C GLU* 3.3 19.0 - - + +
83C LYS* 2.8 64.0 + - + +
110C LEU* 5.8 0.2 - - + -
113C SER* 3.6 31.0 - - - +
122C HIS* 4.3 14.6 - - + -
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Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASN 4.8 2.9 - - - -
48C ASP 3.8 9.4 - - - -
49C VAL* 3.0 43.5 - - + -
50C PRO* 3.3 24.9 - - + -
76C GLN 3.0 12.0 + - - +
77C GLY 2.6 16.3 + - - +
79C ILE* 1.3 71.1 - - - +
81C TYR* 1.3 70.7 + + - -
83C LYS* 3.2 8.1 + - + +
84C LEU* 2.9 54.1 + - + +
129C PRO* 5.5 12.6 - - + -
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Residues in contact with TYR 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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49C VAL* 2.7 32.4 - - + +
50C PRO 4.4 1.1 - - - -
77C GLY* 2.6 33.3 + - - +
78C LEU* 4.2 2.2 - - + +
80C PHE* 1.3 75.2 - + - +
82C GLU* 1.3 57.0 + - - +
84C LEU* 2.7 35.4 + - + +
85C LEU* 3.0 17.1 + - + +
109C LEU* 4.0 4.7 - - + -
146C ILE* 3.6 17.7 - - + -
149C SER* 2.3 39.9 + - - -
150C LEU* 3.6 46.2 - - + -
153C PHE* 3.7 32.0 - + + +
154C VAL* 6.1 0.2 - - + -
181D GLU* 3.7 4.7 + - - -
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Residues in contact with GLU 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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78C LEU 2.5 32.8 + - - +
79C ILE* 3.3 27.5 - - + +
81C TYR* 1.3 73.1 - - - +
83C LYS* 1.3 73.3 + - - +
85C LEU* 3.6 3.4 + - - +
106C HIS* 2.8 39.1 + - - +
109C LEU* 3.5 31.0 - - + +
110C LEU* 2.8 43.8 - - - +
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Residues in contact with LYS 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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79C ILE* 2.8 46.2 + - - +
80C PHE* 3.4 7.6 - - + +
82C GLU* 1.3 83.4 - - - +
84C LEU* 1.3 57.3 + - + +
86C GLY* 2.6 33.0 + - - -
87C SER* 3.2 4.8 + - - -
106C HIS* 5.2 0.4 - - - -
122C HIS* 3.8 24.7 - - - +
129C PRO* 4.8 27.6 - - + +
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C VAL* 5.7 0.7 - - + -
80C PHE* 2.9 51.4 + - + +
81C TYR* 2.7 22.7 + - + +
83C LYS* 1.3 71.8 - - + +
85C LEU* 1.3 63.6 + - + +
86C GLY 3.0 0.4 + - - -
87C SER* 2.6 31.7 + - - +
89C ILE* 4.8 15.0 - - + -
90C PHE* 3.2 9.8 - - + -
129C PRO* 5.1 14.4 - - + -
130C SER* 6.0 1.1 - - - +
146C ILE* 3.2 39.0 - - + -
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Residues in contact with LEU 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 TYR* 3.0 28.8 + - + +
82C GLU 4.0 2.7 - - - +
83C LYS 3.0 0.6 + - - -
84C LEU* 1.3 80.0 - - + +
86C GLY* 1.3 63.3 + - - +
90C PHE* 3.5 34.8 - - + +
91C THR* 4.7 0.7 + - - -
102C VAL* 3.6 27.2 - - + +
105C LEU* 3.4 35.4 - - + -
106C HIS* 3.4 36.0 - - + +
109C LEU* 4.3 8.1 - - + -
146C ILE* 4.8 4.7 - - + -
147C LEU* 5.3 3.6 - - + -
150C LEU* 4.7 7.6 - - + -
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Residues in contact with GLY 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LYS* 2.6 17.9 + - - -
85C LEU* 1.3 70.7 - - - +
87C SER* 1.3 70.3 + - - +
91C THR* 2.9 17.0 + - - -
106C HIS* 3.5 18.3 + - - -
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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
----------------------------------------------------------
83C LYS 3.2 5.6 + - - -
84C LEU* 2.6 30.1 + - - -
85C LEU 3.9 0.3 - - - +
86C GLY* 1.3 84.4 - - - +
88C ASP* 1.3 56.7 + - - +
89C ILE* 2.7 45.4 + - - +
90C PHE* 3.0 9.2 + - - -
91C THR* 3.2 2.6 + - - -
129C PRO* 5.7 7.4 - - - -
131C LEU* 6.2 7.2 - - - -
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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
------------------------------------------------------------
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