Contacts of the strand formed by residues 70 - 78 (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 LEU 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.1 9.9 - - + -
63C TYR* 3.8 16.4 - - + -
64C VAL* 3.6 31.0 - - - +
65C TYR* 3.8 35.7 - - + +
69C LYS* 1.3 71.4 - - - +
71C PHE* 1.3 61.5 + - - +
92C PRO* 3.1 9.6 - - - +
93C VAL* 2.8 46.5 + - + +
94C PRO 3.7 10.1 - - - +
95C PRO* 3.6 33.2 - - + -
96C PRO* 4.0 4.0 - - + -
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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
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29C TYR* 3.6 38.1 - + + -
32C LEU* 4.4 15.9 - - + -
63C TYR* 3.5 3.7 - - - -
64C VAL* 2.8 39.1 + - + +
66C ALA* 3.8 13.7 - - + -
69C LYS* 3.4 35.2 - - + -
70C LEU* 1.3 75.6 - - - +
72C ARG* 1.3 61.9 + - - +
73C ALA 4.0 0.2 - - - -
89C PHE* 3.3 41.3 - + + -
90C ASN 3.2 20.9 - - - +
91C GLY* 3.7 15.0 - - - -
92C PRO* 3.8 13.5 - - + -
93C VAL* 4.4 4.3 - - - -
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Residues in contact with ARG 72 (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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61C GLN* 2.6 59.4 + - + +
62C LEU 3.3 13.7 - - - +
63C TYR* 4.5 19.5 - - + -
71C PHE* 1.3 73.9 - - - +
73C ALA* 1.3 59.7 + - - +
74C ASP* 3.2 35.5 + - - +
88C ARG* 4.0 8.4 - - - +
89C PHE* 3.7 1.4 - - - -
90C ASN* 2.9 52.6 + - + +
93C VAL* 4.4 14.5 - - + +
63D TYR* 3.2 13.6 + - - -
72D ARG* 6.1 3.4 - - - +
94D PRO* 5.5 6.6 + - - +
95D PRO 5.5 3.6 + - - -
96D PRO* 5.2 2.6 - - - +
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Residues in contact with ALA 73 (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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19C ALA* 3.8 20.9 - - + -
60C TYR 3.5 1.4 - - - +
61C GLN* 3.4 4.5 - - - +
62C LEU* 2.9 40.1 + - + +
64C VAL* 4.3 9.6 - - + -
71C PHE 3.9 0.6 + - - -
72C ARG* 1.3 76.5 - - - +
74C ASP* 1.3 61.2 + - - +
75C ILE* 4.1 5.6 - - + -
86C LEU* 4.6 0.7 - - + -
88C ARG 3.4 4.9 - - - +
89C PHE* 3.8 25.1 - - + -
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Residues in contact with ASP 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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3C TRP* 5.4 0.5 - - - -
59C GLU* 2.8 26.4 - - - +
60C TYR 3.3 4.9 - - - -
61C GLN* 4.0 11.1 - - - +
72C ARG* 3.2 36.9 + - - +
73C ALA* 1.3 72.7 - - - +
75C ILE* 1.3 57.1 + - - +
87C LEU* 2.7 48.5 + - + +
88C ARG* 2.8 34.7 + - + +
95D PRO 5.5 1.8 - - - -
96D PRO* 5.0 7.9 - - - +
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Residues in contact with ILE 75 (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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15C LEU* 3.3 48.7 - - + +
18C PHE* 4.2 14.6 - - + -
19C ALA* 3.7 21.3 - - + +
59C GLU* 3.4 2.4 - - - +
60C TYR* 2.7 50.5 + - + +
62C LEU* 4.0 19.1 - - + -
73C ALA* 4.7 2.2 - - + -
74C ASP* 1.3 79.2 - - - +
76C SER* 1.3 71.9 + - - +
84C ARG* 4.6 2.0 - - + -
85C LYS 3.3 17.0 - - - +
86C LEU* 4.3 8.7 - - + -
87C LEU* 4.1 4.0 - - - -
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Residues in contact with SER 76 (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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58C TYR 3.4 9.4 - - - -
59C GLU* 4.5 3.1 - - - +
60C TYR* 5.1 0.2 - - - -
75C ILE* 1.3 82.6 - - - +
77C GLU* 1.3 62.6 + - - +
78C ASP 4.3 0.2 - - - -
83C GLY 4.4 0.7 - - - -
84C ARG* 3.3 5.0 - - - -
85C LYS* 3.2 36.5 + - - +
87C LEU* 3.6 31.2 - - - +
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Residues in contact with GLU 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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11C PHE* 4.3 5.5 - - - -
43C LYS* 5.0 0.2 + - - -
57C GLY* 3.3 2.8 - - - -
58C TYR* 3.0 48.0 + - + +
60C TYR* 2.7 40.9 + - + -
75C ILE* 5.8 0.2 - - + -
76C SER* 1.3 77.3 - - - +
78C ASP* 1.3 73.9 + - - +
82C ARG* 4.6 17.8 + - - +
83C GLY 3.3 7.4 - - - +
84C ARG* 3.0 40.5 + - + +
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Residues in contact with ASP 78 (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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56C LYS* 3.9 17.6 + - - +
57C GLY* 4.5 0.4 - - - -
77C GLU* 1.3 78.4 - - - +
79C TYR* 1.3 60.6 + - - +
80C LYS* 3.4 8.6 + - - +
81C THR* 2.9 49.5 + - - +
82C ARG* 2.9 28.1 + - - +
83C GLY* 2.8 13.9 + - - +
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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