Contacts of the strand formed by residues 55 - 72 (chain C) in PDB entry 2C4Y
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 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLN* 3.4 5.7 + - - -
51C SER* 2.9 38.5 + - - +
52C SER* 3.2 24.6 + - - +
54C GLN* 1.3 92.2 - - - +
56C ARG* 1.3 62.8 + - - +
91C THR* 3.6 23.7 - - + +
92C ILE 3.9 1.1 - - - -
93C PRO* 3.4 24.4 - - - +
94C ILE* 4.7 0.4 - - - -
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 5.8 3.2 - - - +
38A ARG* 3.9 50.3 - - - +
48C VAL* 3.7 26.9 - - + +
49C ARG 3.2 9.2 - - - +
50C GLN* 3.6 26.9 - - - +
51C SER* 4.4 0.2 - - - -
55C ASN* 1.3 74.9 - - - +
57C LYS* 1.3 62.3 + - - +
58C TYR* 3.0 33.5 + - + -
90C LEU 3.9 0.7 - - - +
91C THR* 3.6 2.8 - - - +
92C ILE* 3.0 45.7 + - + +
94C ILE* 4.5 9.6 - - + +
101C CYS* 5.8 5.3 - - - -
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Residues in contact with LYS 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL* 3.5 3.1 - - - -
49C ARG* 2.7 60.6 + - - +
51C SER* 3.7 24.7 - - - +
56C ARG* 1.3 76.0 - - - +
58C TYR* 1.3 70.7 + - - +
89C GLU* 3.1 47.6 + - - -
90C LEU 3.4 6.1 - - - +
91C THR* 3.9 20.2 - - - +
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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
----------------------------------------------------------
46C CYS* 4.7 13.0 - - - -
47C SER 3.3 7.6 - - - -
48C VAL* 3.6 37.0 - - + +
56C ARG* 3.0 31.6 + - + -
57C LYS* 1.3 75.5 - - - +
59C THR* 1.3 61.0 + - - +
60C ILE* 4.1 15.7 - - + -
88C MET 4.4 0.2 - - - -
89C GLU* 3.2 7.3 - - - +
90C LEU* 2.8 54.1 + - + +
92C ILE* 4.1 24.7 - - + -
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Residues in contact with THR 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C CYS* 3.4 1.4 - - - -
47C SER* 3.0 25.7 + - - -
49C ARG* 3.1 30.8 + - - -
57C LYS 3.9 0.2 + - - -
58C TYR* 1.3 73.3 + - - +
60C ILE* 1.3 62.7 + - - +
61C LYS* 4.3 17.5 - - + -
87C ASN* 5.3 1.8 - - - +
88C MET 3.5 6.3 - - - +
89C GLU* 3.5 17.7 + - + +
12S A 3.0 43.9 + - + +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 5.0 6.3 - - + -
45C THR 3.4 9.6 - - - +
46C CYS* 4.1 20.2 - - + -
58C TYR* 4.6 15.3 - - + -
59C THR* 1.3 80.4 - - - +
61C LYS* 1.3 74.9 + - - +
62C VAL* 4.7 10.1 - - + -
86C LEU* 4.0 1.0 - - + +
87C ASN* 3.7 0.3 - - - +
88C MET* 2.8 72.3 + - + +
90C LEU* 5.8 4.9 - - + +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS 3.8 0.4 - - - +
44C VAL* 3.2 6.2 - - - +
45C THR* 2.9 43.7 + - + +
59C THR* 4.3 12.3 - - + -
60C ILE* 1.3 77.3 - - - +
62C VAL* 1.3 65.4 - - - +
63C GLU* 6.4 0.7 - - + -
86C LEU* 3.3 7.6 - - - +
87C ASN* 3.2 29.0 + - - +
9S A 5.1 4.0 + - - +
11S SUR 4.3 24.2 + - - +
12S A 3.3 55.5 + - + +
13S C 5.2 8.5 - - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.4 26.0 - - + -
43C LYS 3.3 7.9 - - - +
44C VAL* 4.3 16.4 - - + -
60C ILE* 4.7 8.5 - - + -
61C LYS* 1.3 81.6 - - - +
63C GLU* 1.3 75.6 + - - +
64C VAL* 4.3 12.3 - - + +
84C SER 3.8 0.2 - - - +
85C TYR* 3.7 3.1 - - - -
86C LEU* 2.9 60.2 + - + +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 4.2 4.9 + - - -
42C TYR* 3.5 14.0 - - - -
43C LYS* 2.9 60.6 + - + +
61C LYS* 6.4 0.9 - - + -
62C VAL* 1.3 77.3 - - - +
64C VAL* 1.3 62.7 + - - +
65C PRO* 3.6 1.1 - - - +
83C ARG* 3.0 35.3 + - - +
84C SER 3.5 3.4 - - - +
85C TYR* 3.7 29.6 - - + -
11S SUR 2.7 28.4 + - - +
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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
----------------------------------------------------------
9C LEU* 5.9 1.1 - - + -
42C TYR* 3.7 26.2 - - + +
62C VAL* 4.4 14.6 - - + -
63C GLU* 1.3 76.1 - - - +
65C PRO* 1.3 69.6 - - + +
82C TRP* 4.7 3.6 - - + -
83C ARG* 3.4 3.4 - - - -
84C SER* 2.8 51.5 + - - +
86C LEU* 6.4 0.7 - - + -
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Residues in contact with PRO 65 (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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40C GLN* 3.3 26.9 - - - +
41C ALA 3.7 7.2 - - - +
42C TYR* 3.7 32.6 + - + -
63C GLU 3.6 9.4 - - - +
64C VAL* 1.3 92.8 - - - +
66C LYS* 1.3 62.9 + - - +
67C VAL* 3.6 7.8 + - + +
80C ALA* 4.1 8.5 - - + -
82C TRP* 3.7 6.7 - - - +
83C ARG* 3.9 25.6 - - + +
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Residues in contact with LYS 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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65C PRO* 1.3 72.1 - - - +
67C VAL* 1.3 68.3 + - - +
68C ALA* 5.6 0.2 - - + -
80C ALA* 3.4 2.7 - - - -
81C ALA* 2.8 38.4 + - + +
82C TRP* 3.0 67.9 + - + +
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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
----------------------------------------------------------
40C GLN* 3.4 48.2 - - + +
42C TYR* 5.8 4.0 - - + -
65C PRO* 3.6 9.5 + - + +
66C LYS* 1.3 80.7 - - - +
68C ALA* 1.3 65.3 + - - +
79C VAL 4.0 4.0 - - - -
80C ALA* 4.8 0.7 - - - +
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Residues in contact with ALA 68 (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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40C GLN* 2.9 21.1 + - - -
66C LYS* 3.3 1.5 + - + -
67C VAL* 1.3 78.4 - - - +
69C THR* 1.3 65.0 + - - +
79C VAL* 2.9 23.6 + - + +
81C ALA* 3.9 28.9 - - + +
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Residues in contact with THR 69 (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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40C GLN* 5.4 0.9 + - - -
68C ALA* 1.3 77.7 + - - +
70C GLN* 1.3 62.6 + - - +
71C THR* 3.8 8.9 + - - +
76C GLU* 3.7 35.9 - - + +
77C LEU 3.6 8.3 - - - +
78C PRO* 5.3 2.6 - - + +
79C VAL* 4.4 1.1 - - - -
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Residues in contact with GLN 70 (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 THR* 1.3 72.4 - - - +
71C THR* 1.3 62.5 - - - +
72C VAL* 3.9 24.7 - - + +
75C VAL 3.5 1.9 - - - +
76C GLU* 3.0 3.3 - - - -
77C LEU* 2.8 59.1 + - - +
79C VAL* 3.7 32.2 - - + +
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Residues in contact with THR 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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69C THR* 3.8 8.7 + - - +
70C GLN* 1.3 75.4 - - - +
72C VAL* 1.3 71.4 + - - +
74C GLY* 4.0 24.5 - - - +
75C VAL 3.4 9.6 - - - +
76C GLU* 3.5 22.4 + - + +
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Residues in contact with VAL 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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70C GLN* 3.9 27.8 - - + +
71C THR* 1.3 82.3 - - - +
73C GLY* 1.3 65.0 + - - +
75C VAL* 2.9 35.1 + - - +
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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