Contacts of the strand formed by residues 45 - 53 (chain B) in PDB entry 2NQY
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 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TRP* 3.8 18.2 - - + -
20B LYS* 3.2 20.1 - - - +
21B ASP* 2.9 40.8 + - - +
43B VAL* 4.5 3.4 - - - +
44B SER* 1.3 81.1 + - - +
46B ILE* 1.3 60.6 + - - +
47B LEU* 5.1 1.6 - - + -
184B GLU* 4.4 8.3 + - - -
185B GLY 3.7 3.8 + - - -
186B TYR* 3.1 20.9 - - - -
3002B XYP 2.8 34.3 + - - -
1D XYP 4.9 7.7 + - - -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 3.9 14.1 - - + -
19B TRP 3.3 11.7 - - - +
20B LYS* 3.7 13.7 - - + -
26B GLY* 3.7 22.0 - - - -
40B TRP* 3.9 7.9 - - + -
43B VAL* 3.7 29.6 - - + -
45B ASN* 1.3 75.9 - - - +
47B LEU* 1.3 69.9 + - - +
48B PHE* 3.4 39.0 - - + -
184B GLU* 3.3 7.8 - - - +
185B GLY* 2.9 44.4 + - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU 3.9 1.2 - - - +
18B PHE* 3.7 4.5 - - - -
19B TRP* 2.7 47.1 + - + +
45B ASN* 5.1 0.7 - - + -
46B ILE* 1.3 86.4 - - - +
48B PHE* 1.3 66.5 + - - +
49B ARG* 3.8 12.8 - - - +
85B TYR* 3.5 35.9 - - + +
182B THR* 4.2 10.1 - - + -
183B VAL 3.4 3.8 - - - +
184B GLU* 3.9 22.0 - - + +
1D XYP 3.5 28.0 - - - +
2D XYP 3.5 19.5 - - - +
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU 3.8 4.3 - - - -
18B PHE* 3.9 23.1 - + - -
27B THR 3.7 18.2 - - - -
28B MET* 3.6 24.9 - - + -
36B PHE* 3.7 21.6 - - + -
38B ALA* 3.6 15.3 - - + -
39B SER 3.3 21.3 - - - -
40B TRP* 3.8 20.9 - + + -
46B ILE* 3.4 33.9 - - + -
47B LEU* 1.3 75.8 - - - +
49B ARG* 1.3 64.1 + - - +
182B THR* 3.2 2.1 - - - +
183B VAL* 2.7 51.6 + - + +
185B GLY 5.6 0.2 - - - -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP 5.3 0.9 - - - +
16B TYR* 3.2 4.5 - - - -
17B GLU* 2.9 66.5 + - - +
19B TRP* 4.4 1.8 - - - +
28B MET* 3.4 12.0 - - - +
36B PHE* 4.0 2.9 - - - -
47B LEU* 3.8 15.4 - - - +
48B PHE* 1.3 77.7 - - - +
50B LYS* 1.3 61.3 + - - +
53B LYS* 4.6 0.6 - - - +
85B TYR* 3.8 16.6 - - - -
87B TRP* 4.7 2.6 - - - +
177B TYR* 4.9 1.4 - - - -
178B GLU* 2.8 43.3 + - - +
180B ALA* 3.8 5.6 - - + -
181B LEU 3.3 7.4 - - - +
182B THR* 3.2 27.4 - - - +
2D XYP 2.9 44.5 + - - -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B HIS* 2.8 34.9 + - - -
14B TYR* 4.0 10.8 - - + -
15B ASP 3.2 4.3 - - - -
16B TYR* 3.7 13.9 - - + -
28B MET* 4.7 1.1 - - + -
30B LEU* 4.1 12.1 - - - -
31B ASN 2.8 25.5 + - - +
33B GLY 2.8 22.7 + - - +
34B GLY* 3.4 29.2 - - - +
35B THR 3.0 12.0 + - - +
36B PHE* 3.7 9.7 - - + -
49B ARG* 1.3 77.8 - - - +
51B GLY* 1.3 57.3 + - - +
180B ALA* 3.7 4.3 - - - -
181B LEU 3.2 17.9 + - - -
197B ASN* 3.2 18.6 + - - +
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 3.6 12.5 - - - -
15B ASP 2.9 29.7 + - - -
50B LYS* 1.3 75.1 - - - +
52B LYS* 1.3 60.1 + - - -
68B ILE* 6.4 0.7 - - - -
179B VAL 3.3 12.3 - - - -
180B ALA* 3.7 4.8 - - - +
181B LEU 4.8 0.2 - - - -
199B LEU* 4.3 5.6 - - - -
206B LEU* 3.3 16.5 - - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 6.0 1.4 - - - +
15B ASP* 3.6 10.3 + - - +
51B GLY* 1.3 72.6 - - - +
53B LYS* 1.3 77.3 + - - +
54B PHE* 3.6 35.3 - - + -
178B GLU* 3.3 5.0 - - - +
179B VAL 2.7 38.8 + - - +
180B ALA* 4.7 0.6 - - - +
199B LEU* 3.5 21.5 - - + +
201B ILE* 4.5 4.3 - - + -
206B LEU* 4.1 22.6 - - + +
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 4.6 19.0 + - + +
15B ASP* 2.8 29.3 + - + +
16B TYR 4.5 6.5 + - - -
17B GLU* 3.0 38.9 + - - +
52B LYS* 1.3 93.3 + - - +
54B PHE* 1.3 63.4 + - - +
177B TYR* 3.4 35.2 - - + +
178B GLU* 3.1 28.9 + - + -
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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