Contacts of the strand formed by residues 55 - 68 (chain C) in PDB entry 5VSU
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 GLU 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C LEU* 4.1 4.5 - - - +
52C ASN* 2.8 38.2 + - + +
53C ASN 3.7 0.2 - - - -
54C GLU* 1.3 79.3 - - - +
56C LEU* 1.3 72.2 - - - +
57C SER* 3.7 1.5 + - - -
102H LYS* 5.1 0.2 - - - +
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Residues in contact with LEU 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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49C TYR* 4.6 4.0 - - + -
50C GLN 3.7 17.0 - - - +
51C LEU* 4.3 4.6 - - + +
55C GLU* 1.3 82.2 - - - +
57C SER* 1.3 66.1 + - - +
58C GLU* 5.1 8.0 - - - +
99H ILE* 3.9 24.0 - - + +
102H LYS* 3.4 57.6 - - + +
103H VAL* 3.5 17.9 - - + +
106H SER* 3.8 15.3 - - - +
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR* 3.6 2.9 - - - -
50C GLN* 2.8 58.6 + - - +
52C ASN* 5.3 7.6 - - - -
55C GLU* 3.7 4.9 + - - -
56C LEU* 1.3 78.9 - - - +
58C GLU* 1.3 70.0 + - - +
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Residues in contact with GLU 58 (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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47C THR* 4.4 6.1 - - + +
48C ILE 3.2 6.7 - - - +
49C TYR* 3.6 37.9 + - + -
50C GLN* 5.5 2.7 - - - -
56C LEU* 5.1 6.8 - - - +
57C SER* 1.3 84.4 + - - +
59C SER* 1.3 65.9 + - - +
60C GLU* 4.9 5.7 - - - +
106H SER* 4.5 12.0 + - - -
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Residues in contact with SER 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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47C THR* 3.5 6.4 - - - +
48C ILE* 3.0 45.4 + - - +
50C GLN* 5.7 3.3 + - - -
58C GLU* 1.3 77.8 - - - +
60C GLU* 1.3 65.4 + - - +
61C ARG* 5.8 1.5 - - - +
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Residues in contact with GLU 60 (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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45C VAL* 3.6 19.6 - - + +
46C GLU 3.3 15.7 - - - +
47C THR* 3.2 19.9 + - - +
48C ILE* 6.1 0.2 - - - -
58C GLU* 4.9 5.7 - - - +
59C SER* 1.3 80.0 - - - +
61C ARG* 1.3 70.0 + - - +
62C ARG* 3.5 30.4 + - + +
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Residues in contact with ARG 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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18B GLU* 3.3 10.1 + - - -
24B GLU* 2.6 39.4 + - - -
71B TYR* 3.8 27.8 + - + +
45C VAL* 3.4 1.2 - - - +
46C GLU* 2.8 56.5 + - + +
48C ILE* 5.0 12.6 - - + -
59C SER* 5.8 1.3 - - - +
60C GLU* 1.3 78.2 - - - +
62C ARG* 1.3 70.1 + - - +
63C CYS* 5.8 1.1 - - - -
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Residues in contact with ARG 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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44C ALA 3.5 7.9 - - - +
45C VAL* 3.4 27.3 - - + +
60C GLU* 3.5 27.1 + - + +
61C ARG* 1.3 83.1 - - - +
63C CYS* 1.3 65.6 + - - +
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Residues in contact with CYS 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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71B TYR* 3.9 28.5 - - + -
72B LEU 6.0 0.2 - - - +
26C LEU* 5.4 3.1 - - - -
43C ASP* 3.5 2.6 - - - -
44C ALA* 2.9 44.8 + - - +
45C VAL* 5.9 0.2 - - - -
46C GLU* 5.9 2.7 - - - -
61C ARG* 5.8 1.1 - - - -
62C ARG* 1.3 79.4 - - - +
64C GLU* 1.3 63.1 + - - +
65C MET 4.6 2.7 - - - +
66C VAL* 3.8 35.4 - - - -
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Residues in contact with GLU 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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72B LEU 4.1 7.5 + - - +
73B ASN* 3.5 17.7 - - - +
74B LYS* 3.2 45.7 + - + +
42C SER* 3.3 6.1 - - - -
43C ASP* 2.7 34.8 + - - +
63C CYS* 1.3 75.4 - - - +
65C MET* 1.3 61.6 + - - +
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Residues in contact with MET 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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71B TYR* 3.5 4.2 - - - +
72B LEU* 2.6 66.4 + - + +
73B ASN 4.1 8.1 - - - +
74B LYS* 4.2 14.8 - - + +
77B VAL* 3.3 35.2 - - + -
79B THR* 4.1 15.0 - - + -
82B LEU* 6.0 0.4 - - + -
31C GLN* 4.7 1.6 - - + -
40C VAL* 3.8 17.7 - - + -
41C LEU 3.5 15.0 - - - +
42C SER* 3.5 25.1 - - - -
63C CYS* 3.5 1.1 - - - +
64C GLU* 1.3 81.3 + - - +
66C VAL* 1.3 58.9 + - - +
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Residues in contact with VAL 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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69B TYR* 4.1 17.0 - - + -
70B VAL 3.2 9.0 - - - +
71B TYR* 4.0 21.1 - - + -
72B LEU* 4.8 2.9 - - - -
26C LEU* 4.8 4.0 - - + -
39C ILE 3.7 0.5 - - - +
40C VAL* 3.4 4.0 - - - +
41C LEU* 2.9 49.2 + - + +
44C ALA* 3.8 25.1 - - + -
63C CYS* 3.8 13.7 - - - -
65C MET* 1.3 76.4 - - - +
67C PHE* 1.3 74.8 + - - +
68C ILE* 4.4 9.3 - - + +
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Residues in contact with PHE 67 (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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3B PHE* 3.8 32.3 - + + -
6B PHE* 5.1 0.2 - + - -
7B PHE* 3.8 36.6 - + + -
36B LEU* 4.6 10.5 - - + -
67B VAL* 4.7 8.7 - - + -
69B TYR* 3.3 7.6 - - - -
70B VAL* 2.6 58.9 + - + +
72B LEU* 4.5 6.9 - - + +
38C ASN* 4.0 31.0 - - + -
39C ILE 3.4 9.2 - - - -
40C VAL* 4.3 7.9 - - + -
66C VAL* 1.3 76.8 - - - +
68C ILE* 1.3 63.8 + - - +
69C ARG* 4.1 20.9 - - + -
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Residues in contact with ILE 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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68B ARG 3.9 2.5 - - - -
69B TYR* 4.0 20.2 - - + -
18C ILE* 4.7 6.7 - - + -
20C LEU* 4.6 4.3 - - + -
26C LEU* 3.5 26.7 - - + -
37C CYS 4.1 0.3 - - - +
38C ASN* 3.2 5.4 - - - +
39C ILE* 2.8 42.1 + - + +
41C LEU* 3.8 27.8 - - + -
66C VAL* 4.4 9.0 - - + +
67C PHE* 1.3 82.7 - - - +
69C ARG* 1.3 67.7 + - - +
72C THR* 3.9 19.1 - - - +
73C VAL* 4.2 14.6 - - + -
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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