Contacts of the strand formed by residues 55 - 66 (chain C) in PDB entry 3Q2P
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 ILE 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C THR* 4.3 7.4 - - + -
46C ILE 3.6 8.5 - - - +
47C TYR* 3.8 24.2 - - + +
48C GLU* 4.2 3.9 - - - +
53C ARG 3.7 2.4 + - - +
54C GLU* 1.3 71.7 - - - +
56C LYS* 1.3 62.8 + - - +
57C GLY 3.7 17.9 - - - +
58C TYR* 4.1 19.3 - - + +
79C TYR* 3.7 57.3 - - + +
80C LYS* 5.8 1.2 - - - +
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Residues in contact with LYS 56 (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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46C ILE* 2.6 32.1 + - + +
47C TYR 4.1 10.3 - - - +
48C GLU* 3.2 38.7 + - - +
49C ASN* 5.6 9.0 - - - +
54C GLU 3.2 2.2 + - - -
55C ILE* 1.3 72.8 - - - +
57C GLY* 1.3 56.7 + - - +
78C ASP* 3.9 16.5 + - - +
79C TYR* 3.1 20.8 + - - +
80C LYS 4.6 0.7 + - - -
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 2.9 31.6 + - - +
55C ILE* 3.6 4.9 - - - +
56C LYS* 1.3 83.5 - - - +
58C TYR* 1.3 70.2 + - - -
77C GLU 3.3 13.2 - - - -
78C ASP* 4.5 0.7 - - - -
79C TYR* 3.8 10.3 - - - -
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Residues in contact with TYR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS* 3.4 34.5 - - - -
44C LYS 3.2 7.0 - - - +
45C THR* 3.3 29.4 - - + -
46C ILE* 4.7 4.5 - - - +
55C ILE* 4.1 18.5 - - + +
57C GLY* 1.3 80.1 - - - -
59C GLU* 1.3 63.0 + - - +
60C TYR* 4.0 11.2 - - + -
75C ILE 4.6 0.4 - - - -
76C SER* 3.4 6.1 - - - -
77C GLU* 3.0 53.1 + - + +
79C TYR* 3.5 40.5 - + + -
82C ARG* 5.1 7.1 + - - -
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Residues in contact with GLU 59 (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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3C TRP* 3.7 9.4 - - + -
43C LYS* 3.2 5.0 - - - -
44C LYS* 2.7 78.5 + - + +
46C ILE* 4.2 12.9 - - + +
58C TYR* 1.3 76.4 - - - +
60C TYR* 1.3 61.5 + - - +
74C ASP* 2.8 26.2 - - - +
75C ILE 3.4 5.8 - - - +
76C SER* 4.5 3.4 - - - -
87C LEU* 3.8 23.5 - - + +
96D PRO 3.9 15.6 - - - +
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TRP* 4.8 2.2 - - - -
6C ILE* 4.3 16.2 - - + -
11C PHE* 3.9 11.3 - + - -
15C LEU* 3.6 37.0 - - + -
42C MET 3.4 4.7 - - - +
43C LYS* 3.2 53.5 + - + -
58C TYR* 4.0 6.9 - - + +
59C GLU* 1.3 75.8 - - - +
61C GLN* 1.3 59.0 + - - +
62C LEU* 3.3 20.4 - - + -
73C ALA 3.5 1.0 - - - +
74C ASP* 3.3 7.9 - - - -
75C ILE* 2.7 54.4 + - + +
77C GLU* 2.7 45.0 + - + -
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Residues in contact with GLN 61 (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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3C TRP* 4.2 8.5 - - + -
40C PRO 4.4 1.7 - - - +
41C CYS* 3.6 2.6 - - - -
42C MET* 3.0 65.2 + - + +
60C TYR* 1.3 72.6 - - - +
62C LEU* 1.3 60.8 + - - +
63C TYR* 5.1 9.4 + - + -
72C ARG* 2.6 56.5 + - + +
73C ALA 3.4 2.9 - - - -
74C ASP* 4.0 8.1 - - - +
42D MET* 4.9 7.5 - - - +
61D GLN* 5.2 2.6 - - - +
63D TYR* 3.0 20.1 + - - -
72D ARG* 5.5 4.4 - - - +
96D PRO* 4.4 7.3 - - - +
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Residues in contact with LEU 62 (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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6C ILE* 6.0 0.4 - - + -
12C THR* 4.1 9.4 - - + +
15C LEU* 3.8 15.5 - - + -
16C ALA* 3.7 39.0 - - + +
37C ALA* 5.1 0.7 - - + -
41C CYS* 3.9 21.3 - - + -
42C MET 4.7 1.3 - - - +
60C TYR* 3.3 39.7 - - + +
61C GLN* 1.3 76.5 - - - +
63C TYR* 1.3 69.6 + - - +
64C VAL* 5.3 1.1 - - + -
72C ARG* 3.3 11.4 - - - +
73C ALA* 2.9 40.4 + - + +
75C ILE* 4.0 11.2 - - + -
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Residues in contact with TYR 63 (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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37C ALA* 3.2 10.2 - - - +
38C ILE* 3.1 43.2 + - + +
40C PRO* 3.3 40.8 - - + -
41C CYS* 3.9 4.4 - - - -
61C GLN* 5.1 8.3 + - - -
62C LEU* 1.3 77.2 - - - +
64C VAL* 1.3 59.5 + - - +
70C LEU* 3.8 23.8 - - + -
71C PHE 3.5 3.1 - - - -
72C ARG* 4.5 16.9 - - + +
93C VAL* 4.2 18.8 - - + -
94C PRO 4.3 4.7 - - - -
96C PRO* 4.0 17.9 - - + +
42D MET* 5.8 0.9 - - + -
61D GLN* 2.9 29.2 + - - -
72D ARG* 3.1 15.1 + - - -
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Residues in contact with VAL 64 (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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16C ALA* 3.9 29.4 - - + +
20C VAL* 4.2 9.4 - - + -
34C PHE* 3.9 11.7 - - + -
36C LYS 3.4 9.6 - - - +
37C ALA* 4.0 0.2 - - - +
62C LEU* 5.3 1.6 - - + -
63C TYR* 1.3 76.1 - - - +
65C TYR* 1.3 76.8 + - - +
66C ALA 3.8 0.3 + - - -
69C LYS 3.4 2.1 - - - +
70C LEU* 3.7 6.2 - - - +
71C PHE* 2.8 49.5 + - + +
73C ALA* 4.3 12.8 - - + -
89C PHE* 4.2 25.6 - - + -
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASN* 2.8 44.6 + - + +
36C LYS* 2.6 42.0 + - + +
38C ILE* 4.0 23.6 - - + +
64C VAL* 1.3 79.5 - - - +
66C ALA* 1.3 54.7 + - - +
68C ASP* 4.1 7.9 - - - -
69C LYS* 3.2 23.3 - - - -
70C LEU* 3.8 40.3 - - + +
95C PRO* 4.3 15.2 - - - +
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Residues in contact with ALA 66 (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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20C VAL* 4.0 24.5 - - + -
32C LEU* 4.2 19.8 - - + +
33C THR 3.3 11.9 - - - +
35C ASN* 3.1 2.8 + - - -
64C VAL* 3.8 1.1 + - + -
65C TYR* 1.3 75.1 - - - +
67C SER* 1.3 71.0 + - - +
68C ASP 3.2 0.2 - - - -
69C LYS* 2.8 23.8 + - - +
71C PHE* 3.8 17.7 - - + -
89C PHE* 5.1 0.2 - - + -
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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