Contacts of the strand formed by residues 39 - 49 (chain C) in PDB entry 5NXR
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 ARG 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C LYS* 5.1 4.8 - - - +
18C ASP* 2.8 66.2 + - + +
19C VAL* 5.6 0.2 - - - +
20C ARG* 3.2 35.9 - - - +
37C ASP* 2.2 49.1 + - - -
38C SER* 1.3 76.1 - - - +
40C VAL* 1.3 67.4 + - - +
63C GLU* 4.1 25.4 + - + +
64C THR 3.2 13.9 - - - +
65C LYS* 3.6 24.5 - - + +
66C THR* 3.9 3.1 - - - -
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Residues in contact with VAL 40 (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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60A PHE* 3.7 49.6 - - + -
80A ALA* 3.9 11.0 - - + -
16C LYS 3.4 11.2 - - - +
17C VAL* 4.3 15.5 - - + -
39C ARG* 1.3 81.6 - - - +
41C ARG* 1.3 69.7 + - - +
42C LEU* 4.4 7.6 - - + -
62C TRP* 5.0 0.8 - - + -
63C GLU* 3.1 7.5 - - - +
64C THR* 2.9 42.4 + - + +
66C THR* 3.8 14.1 - - + -
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 4.7 8.9 - - + -
15C GLY* 2.9 4.2 - - - -
16C LYS* 2.7 75.4 + - + +
40C VAL* 1.3 75.2 - - - +
42C LEU* 1.3 76.1 + - - +
61C GLU* 4.0 26.5 + - + -
62C TRP* 3.2 13.5 - - - +
63C GLU* 2.8 28.4 + - - +
78C ARG* 3.1 37.6 - - - +
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Residues in contact with LEU 42 (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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44A VAL* 4.5 15.5 - - + -
60A PHE* 4.1 16.4 - - + -
14C TYR* 3.6 4.5 - - - +
16C LYS 6.1 0.2 - - - -
40C VAL* 4.4 11.2 - - + -
41C ARG* 1.3 86.6 - - - +
43C GLY* 1.3 58.6 + - - +
60C PHE* 5.6 0.6 - - - -
61C GLU* 3.6 2.9 - - - +
62C TRP* 2.8 66.8 + - + +
352C PHE* 4.3 23.6 - - + -
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Residues in contact with GLY 43 (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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13C VAL* 3.5 2.8 - - - +
14C TYR* 2.8 58.1 + - - +
42C LEU* 1.3 77.1 - - - +
44C VAL* 1.3 69.7 + - - +
60C PHE* 3.2 12.6 - - - -
61C GLU* 4.3 0.2 - - - -
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Residues in contact with VAL 44 (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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17B VAL* 5.8 3.4 - - + -
42B LEU* 4.7 12.6 - - + -
352B PHE* 4.6 26.9 - - + -
11C LEU* 5.5 5.6 - - + -
12C ASP 3.4 5.2 - - - +
13C VAL* 3.8 23.6 - - + -
14C TYR* 3.9 2.2 - - - -
43C GLY* 1.3 79.5 - - - +
45C LYS* 1.3 60.6 + - - +
46C GLY 4.4 0.4 - - - -
58C GLY 4.7 0.2 - - - -
59C ARG* 3.3 3.5 - - - +
60C PHE* 2.8 61.5 + - + +
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Residues in contact with LYS 45 (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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10C LYS* 4.0 4.1 - - - +
11C LEU* 3.7 5.0 - - - +
12C ASP* 2.8 71.1 + - + +
14C TYR* 4.2 14.6 - - + -
44C VAL* 1.3 76.0 - - - +
46C GLY* 1.3 58.2 + - - +
47C ASP* 5.0 6.3 - - - +
58C GLY 3.3 9.6 - - - +
59C ARG* 4.0 28.7 - - + +
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Residues in contact with GLY 46 (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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350B TYR* 3.2 25.3 - - - -
10C LYS 3.2 8.7 - - - -
11C LEU* 3.8 6.6 - - - +
45C LYS* 1.3 73.2 - - - +
47C ASP* 1.3 62.8 - - - +
57C PHE* 3.1 7.8 - - - +
58C GLY 2.8 35.6 + - - +
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Residues in contact with ASP 47 (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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350B TYR* 3.9 1.8 - - - -
9C ASN* 3.3 7.3 - - - +
10C LYS* 2.8 58.1 + - + +
45C LYS* 5.0 7.1 - - - +
46C GLY* 1.3 80.4 + - - +
48C THR* 1.3 61.6 + - - +
55C THR* 5.3 10.8 + - + +
56C GLY 3.3 7.8 - - - +
57C PHE* 4.6 8.8 - - - +
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Residues in contact with THR 48 (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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313B ASN* 3.2 20.4 + - - +
315B ASN* 3.4 28.8 + - + +
316B MET* 4.0 14.6 - - + -
350B TYR* 3.9 14.6 - - + -
8C GLY 2.9 16.8 + - - -
9C ASN* 4.4 0.7 - - - -
47C ASP* 1.3 75.8 - - - +
49C GLN* 1.3 57.9 + - - +
50C ILE* 3.4 3.0 + - + -
55C THR* 3.1 10.2 - - - -
56C GLY* 2.7 57.6 + - - +
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Residues in contact with GLN 49 (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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313B ASN* 3.8 9.1 + - - -
8C GLY* 3.1 31.1 + - - +
48C THR* 1.3 70.1 - - - +
50C ILE* 1.3 60.4 + - - +
51C THR 2.6 29.0 + - - +
52C ASP* 3.7 18.0 + - - +
53C GLN 5.1 0.4 - - - -
54C LEU 4.0 0.4 + - - -
55C THR* 3.4 26.1 - - - +
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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