Contacts of the strand formed by residues 49 - 58 (chain Q) in PDB entry 1NVU
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 49 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2Q THR* 5.4 7.8 + - - +
45Q VAL* 3.8 3.1 - - - +
46Q ILE 2.7 37.2 + - - +
47Q ASP 4.2 4.0 - - - +
48Q GLY* 1.3 83.9 - - - +
50Q THR* 1.3 70.3 + - - +
51Q CYS* 3.4 4.2 + - - -
164Q ARG* 3.7 25.9 + - - +
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Residues in contact with THR 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET* 3.2 35.0 - - - +
2Q THR* 3.8 4.7 + - - -
43Q GLN* 4.0 13.9 - - + -
44Q VAL 3.8 4.9 - - - +
45Q VAL* 3.7 8.3 - - + +
48Q GLY 4.3 0.4 + - - -
49Q GLU* 1.3 77.6 - - - +
51Q CYS* 1.3 62.7 + - - +
920S ARG 3.2 26.7 - - - +
921S SER* 2.7 33.0 + - - +
922S ILE 4.4 2.5 - - - +
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Residues in contact with CYS 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET* 4.3 4.5 - - - -
2Q THR* 3.5 5.4 - - - -
4Q TYR* 3.6 20.0 - - + -
42Q LYS 3.6 0.5 - - - +
43Q GLN* 3.3 7.1 - - - +
44Q VAL 2.8 40.0 + - - +
46Q ILE* 4.0 18.2 - - + -
49Q GLU 3.5 10.5 - - - -
50Q THR* 1.3 75.4 - - - +
52Q LEU* 1.3 59.3 + - - +
53Q LEU* 3.7 15.9 - - + -
160Q VAL* 4.3 0.4 - - - -
164Q ARG* 2.8 34.5 - - - -
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Residues in contact with LEU 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET* 4.0 23.3 - - + -
2Q THR 2.9 12.5 + - - +
3Q GLU* 3.2 19.5 - - + +
4Q TYR 2.9 25.8 + - - -
41Q ARG* 3.3 57.9 - - + +
42Q LYS 3.6 12.6 - - - +
43Q GLN* 4.2 9.9 - - + +
51Q CYS* 1.3 74.2 - - - +
53Q LEU* 1.3 61.6 + - - +
54Q ASP* 4.4 0.9 - - - +
920S ARG* 6.3 0.7 - - - +
973S GLN* 5.1 4.0 - - + +
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Residues in contact with LEU 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q TYR* 3.7 10.8 - - + -
6Q LEU* 4.1 16.4 - - + -
23Q LEU* 4.8 2.9 - - + -
40Q TYR 3.6 0.7 - - - +
41Q ARG* 3.2 7.6 - - - +
42Q LYS* 2.8 53.7 + - + +
44Q VAL* 3.9 22.0 - - + -
46Q ILE* 4.5 0.7 - - + -
51Q CYS* 3.7 25.8 - - + -
52Q LEU* 1.3 74.2 - - - +
54Q ASP* 1.3 61.2 + - - +
55Q ILE* 3.9 15.6 + - + +
156Q PHE* 5.2 0.9 - - + -
157Q TYR* 4.1 17.3 - - + -
160Q VAL* 3.8 29.4 - - + -
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Residues in contact with ASP 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q GLU* 2.3 43.2 - - - +
4Q TYR 2.8 10.9 + - - +
5Q LYS* 3.5 16.4 + - + +
6Q LEU* 2.8 28.1 + - - +
39Q SER* 5.6 3.8 - - - +
40Q TYR 3.4 5.2 - - - +
41Q ARG* 2.9 41.9 + - - +
52Q LEU* 4.4 0.3 - - - +
53Q LEU* 1.3 71.0 - - - +
55Q ILE* 1.3 61.3 + - - +
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Residues in contact with ILE 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q LEU* 3.4 13.7 - - + +
8Q VAL* 3.9 24.5 - - + -
20Q THR* 3.8 24.7 - - + +
23Q LEU* 3.5 31.9 - - + -
24Q ILE* 4.2 15.7 - - + -
38Q ASP 3.8 0.2 - - - +
39Q SER* 3.4 6.4 + - - -
40Q TYR* 2.8 44.0 + - + +
42Q LYS* 5.2 0.7 - - + -
53Q LEU* 4.3 19.7 - - + +
54Q ASP* 1.3 77.7 - - - +
56Q LEU* 1.3 63.6 + - - +
57Q ASP 3.7 1.0 + - - -
156Q PHE* 3.8 13.2 - - + -
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Residues in contact with LEU 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q LEU 2.8 16.4 + - - +
7Q VAL* 3.5 11.5 - - + +
8Q VAL* 2.9 28.2 + - - +
37Q GLU* 5.1 2.5 - - + -
38Q ASP 3.4 18.2 - - - +
39Q SER* 4.5 4.5 - - - +
54Q ASP 4.0 0.6 + - - -
55Q ILE* 1.3 72.1 - - - +
57Q ASP* 1.3 62.3 + - - +
58Q THR* 3.7 9.8 + - + -
71Q TYR* 3.7 49.8 - - + +
74Q THR* 4.8 6.5 - - - +
619S ALA* 5.7 1.6 - - + -
621S PRO* 3.8 27.6 - - + -
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Residues in contact with ASP 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q VAL* 4.4 5.4 - - - +
16Q LYS* 3.6 23.8 - - - +
17Q SER* 2.6 34.8 + - - -
20Q THR* 4.4 10.0 + - + +
35Q THR* 3.5 12.0 + - - +
37Q GLU* 3.6 3.5 - - - -
38Q ASP* 2.8 43.6 + - + +
40Q TYR* 4.2 20.4 + - + -
55Q ILE 3.7 1.6 + - - -
56Q LEU* 1.3 71.4 - - - +
58Q THR* 1.3 70.5 + - - +
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Residues in contact with THR 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q VAL* 3.8 20.2 - - + -
8Q VAL 2.9 23.5 + - - +
9Q VAL* 3.8 14.7 - - + +
10Q GLY 5.0 0.2 + - - -
16Q LYS* 3.1 22.3 - - - -
35Q THR* 4.0 6.7 - - - -
36Q ILE 4.2 4.0 - - - -
37Q GLU* 4.9 0.9 - - - +
56Q LEU* 4.2 6.5 - - + +
57Q ASP* 1.3 84.6 + - - +
59Q GLY* 1.3 66.1 + - - +
60Q GLY* 5.4 0.3 - - - -
68Q ARG* 5.7 3.3 - - - -
71Q TYR* 3.5 39.9 - - + -
96Q TYR* 6.1 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