Contacts of the helix formed by residues 69 - 90 (chain C) in PDB entry 1T4P
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 ASN 69 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LYS* 3.6 52.7 + - + +
19C GLN 5.8 0.8 + - - -
61C ASP* 3.0 34.1 + - - +
63C PRO* 5.0 1.2 - - - +
68C LYS* 1.3 78.9 - - - +
70C PRO* 1.3 68.6 - - - +
72C SER* 4.4 1.8 + - - -
73C VAL* 3.1 22.7 + - - +
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Residues in contact with PRO 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASP* 3.5 11.9 - - - +
62C SER 3.7 18.8 - - - +
63C PRO* 4.3 0.2 - - + -
64C PHE* 4.3 11.4 - - + -
67C VAL* 3.9 13.2 - - + +
68C LYS 3.0 8.2 - - - +
69C ASN* 1.3 90.4 - - - +
71C ARG* 1.3 64.6 + - + +
73C VAL 3.4 0.2 + - - -
74C GLY 2.8 29.3 + - - -
140C LEU* 4.0 9.4 - - + -
159C VAL* 3.6 28.3 - - + -
160C PRO* 3.3 9.2 - - + +
162C PHE* 3.1 11.8 - - + -
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 3.7 26.9 - - + -
60C ASN 4.8 4.3 - - - -
61C ASP* 2.8 38.8 + - - +
62C SER* 2.8 41.5 + - - +
63C PRO 5.5 1.4 + - - -
64C PHE* 5.9 0.8 - - - +
70C PRO* 1.3 74.3 - - - +
72C SER* 1.3 59.7 + - - +
74C GLY 3.7 0.4 - - - +
75C LYS* 2.8 33.4 + - - +
160C PRO* 3.5 45.6 - - + +
161C GLY* 4.5 5.3 - - - +
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Residues in contact with SER 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.5 7.5 - - - -
17C LYS* 4.5 12.4 + - - -
56C VAL 5.2 3.5 - - - +
57C ASP* 3.5 14.7 + - - -
58C VAL* 3.3 35.2 + - - +
61C ASP* 2.9 19.6 + - - +
69C ASN* 4.0 10.4 + - - +
71C ARG* 1.3 75.9 - - - +
73C VAL* 1.3 57.2 + - - +
75C LYS* 4.1 1.5 - - - +
76C ALA* 3.0 31.0 + - - +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.5 26.2 - - + -
17C LYS* 3.8 21.5 - - + +
18C GLY* 4.1 2.9 - - - +
69C ASN 3.1 19.6 + - - +
70C PRO 3.7 0.4 - - - +
72C SER* 1.3 74.2 - - - +
74C GLY* 1.3 64.3 + - - +
76C ALA* 4.0 0.5 - - - +
77C ASN* 2.8 44.9 + - - +
102C SER* 4.2 9.2 - - - +
105C ILE* 5.1 1.3 - - + -
140C LEU* 3.6 25.1 - - + -
162C PHE* 3.4 20.2 - - + -
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Residues in contact with GLY 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PRO 2.8 16.9 + - - -
71C ARG 3.8 1.1 - - - -
73C VAL* 1.3 78.8 - - - +
75C LYS* 1.3 57.5 + - - +
77C ASN* 3.6 1.0 + - - -
78C GLU 3.1 12.1 + - - -
161C GLY 3.3 22.2 - - - -
162C PHE* 3.7 17.3 - - - -
164C TRP* 2.9 23.4 + - - -
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 4.2 29.4 - - + +
58C VAL* 4.4 12.3 - - + -
71C ARG 2.8 17.5 + - - +
72C SER* 4.1 2.7 - - - +
74C GLY* 1.3 73.6 - - - +
76C ALA* 1.3 66.7 + - - +
77C ASN 3.0 1.3 - - - -
78C GLU* 2.9 35.2 + - - +
79C GLN* 2.9 33.9 + - - +
161C GLY* 4.2 1.0 + - - -
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.5 27.8 - - + -
55C PHE* 3.3 43.1 - - + -
56C VAL 5.8 0.4 + - - -
72C SER 3.0 19.5 + - - +
73C VAL 4.1 2.2 - - - +
75C LYS* 1.3 76.6 - - - +
77C ASN* 1.3 56.0 + - - +
79C GLN* 3.6 2.4 + - - +
80C LEU 3.1 20.1 + - - -
103C MET* 3.6 8.3 - - + +
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Residues in contact with ASN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL* 2.8 39.7 + - - +
74C GLY* 3.9 2.5 - - - +
75C LYS 3.0 0.6 - - - -
76C ALA* 1.3 77.7 - - - +
78C GLU* 1.3 58.6 + - - +
79C GLN 3.2 0.2 - - - -
80C LEU* 3.9 0.9 - - - -
81C ALA 3.1 21.5 + - - -
102C SER* 3.2 20.5 + - - +
103C MET* 3.0 32.7 - - - +
105C ILE* 3.9 8.4 - - + +
106C GLY* 2.8 28.8 + - - +
162C PHE* 5.3 0.7 - - + -
164C TRP* 3.2 25.5 - - + -
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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 GLY 3.1 8.9 + - - +
75C LYS* 2.9 39.3 + - - +
77C ASN* 1.3 73.9 - - - +
79C GLN* 1.3 67.3 + - - +
81C ALA* 3.5 2.8 + - - +
82C ALA* 3.2 20.4 + - - +
113C ARG* 5.2 3.0 + - - +
164C TRP* 3.3 57.2 - - + +
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Residues in contact with GLN 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 4.2 13.3 - - + +
54C ALA 3.0 29.0 + - - +
55C PHE* 3.4 30.4 - - + +
56C VAL* 4.5 10.7 - - - +
75C LYS* 2.9 23.1 + - - +
76C ALA* 3.6 7.0 - - - +
78C GLU* 1.3 78.7 - - - +
80C LEU* 1.3 63.5 + - - +
82C ALA* 3.0 22.8 + - - +
83C VAL* 3.2 13.5 + - + +
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.0 15.9 - - + -
13C ALA* 4.5 4.3 - - + -
53C LEU* 3.8 26.0 - - + +
76C ALA 3.1 15.5 + - - +
77C ASN 4.0 4.5 - - - +
79C GLN* 1.3 78.1 - - - +
81C ALA* 1.3 57.3 + - - +
83C VAL* 3.2 2.2 + - + +
84C VAL* 2.9 43.1 + - + +
96C VAL* 4.3 14.8 - - + -
103C MET* 3.3 50.5 - - + +
106C GLY* 4.3 0.4 - - - -
107C SER* 3.7 17.3 - - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASN 3.1 18.3 + - - +
78C GLU 3.8 5.4 - - - +
79C GLN 3.3 0.2 - - - -
80C LEU* 1.3 76.0 - - - +
82C ALA* 1.3 64.5 + - - +
84C VAL* 4.6 0.2 - - - -
85C ALA* 3.0 22.0 + - - +
106C GLY 3.3 23.7 + - - +
109C SER* 4.2 0.2 - - - -
110C GLY* 3.3 17.7 - - - +
113C ARG* 3.7 10.5 + - - +
164C TRP* 3.8 20.6 - - + -
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Residues in contact with ALA 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 GLU 3.2 10.2 + - - +
79C GLN* 3.0 14.2 + - - +
81C ALA* 1.3 80.8 - - - +
83C VAL* 1.3 65.6 - - + +
85C ALA* 3.2 3.7 + - - +
86C GLU* 3.1 23.0 + - - +
113C ARG* 3.9 10.9 - - - +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.0 20.4 - - + -
50C HIS* 3.4 32.1 - - + +
53C LEU* 3.8 24.0 - - + -
79C GLN* 3.2 16.9 + - + +
80C LEU* 3.6 8.5 - - + +
82C ALA* 1.3 77.8 - - + +
84C VAL* 1.3 62.7 + - - +
86C GLU* 3.0 23.6 + - + +
87C THR* 3.2 13.0 + - + +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.1 14.4 - - + -
80C LEU* 2.9 44.5 + - + +
81C ALA* 4.0 3.8 - - - +
83C VAL* 1.3 72.7 - - - +
85C ALA* 1.3 63.0 + - - +
87C THR* 3.2 7.4 + - - -
88C GLN* 2.9 26.6 + - + +
94C SER* 3.7 20.9 - - - +
96C VAL* 4.2 7.4 - - + -
107C SER* 3.6 31.9 - - - +
110C GLY* 4.3 1.6 - - - -
111C HIS* 3.6 12.3 - - + +
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Residues in contact with ALA 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 ALA 3.0 18.6 + - - +
82C ALA* 3.5 4.9 - - - +
84C VAL* 1.3 77.0 - - - +
86C GLU* 1.3 53.7 + - - +
89C LYS* 2.8 37.5 + - - +
110C GLY* 3.6 20.1 - - - +
113C ARG* 4.1 22.2 - - + +
114C VAL* 3.4 10.8 - - + +
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Residues in contact with GLU 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 ALA 3.1 13.1 + - - +
83C VAL* 3.0 15.2 + - + +
85C ALA* 1.3 77.4 - - - +
87C THR* 1.3 57.4 + - + +
89C LYS* 3.2 45.0 + - - +
90C ASN* 2.4 33.3 + - - +
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Residues in contact with THR 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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9C GLU* 3.0 40.2 - - + +
11C ILE* 4.3 9.3 - - + +
50C HIS* 5.8 0.2 - - + -
83C VAL* 3.2 15.4 + - + +
84C VAL* 3.2 9.9 + - - -
86C GLU* 1.3 78.4 - - + +
88C GLN* 1.3 64.2 + - - +
90C ASN* 3.4 12.0 + - - +
92C THR* 2.9 41.5 + - - +
94C SER* 3.9 20.1 - - - -
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Residues in contact with GLN 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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84C VAL* 2.9 31.3 + - + +
85C ALA* 4.3 0.2 - - - -
87C THR* 1.3 79.6 + - - +
89C LYS* 1.3 67.6 + - - +
91C GLY* 3.1 14.6 + - - -
92C THR 3.5 10.8 + - - +
94C SER* 2.9 24.3 + - - +
111C HIS* 3.6 25.2 + - + -
114C VAL* 3.6 30.0 - - + +
115C HIS* 3.5 25.3 + - - -
271C SER* 2.8 31.0 + - - -
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Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ALA 2.8 15.0 + - - +
86C GLU* 3.2 38.7 + - - +
88C GLN* 1.3 77.4 - - - +
90C ASN* 1.3 63.3 + - + +
91C GLY 3.0 5.7 + - - -
114C VAL* 4.0 15.0 - - + +
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PRO* 5.7 0.7 - - - +
86C GLU* 2.4 43.6 + - - +
87C THR* 3.4 7.5 + - - +
88C GLN 3.3 0.8 - - - -
89C LYS* 1.3 79.3 - - + +
91C GLY* 1.3 59.8 + - - -
92C THR* 3.4 18.2 + - - +
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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