Contacts of the strand formed by residues 54 - 65 (chain B) 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 LEU 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A PHE* 4.1 20.6 - - + -
410A LDA 4.8 12.6 - - + -
50B ILE* 3.0 36.2 + - + +
51B THR* 3.0 44.9 + - + +
53B GLN* 1.3 77.7 - - - +
55B THR* 1.3 60.0 + - - +
84B LEU* 4.1 17.5 - - + -
85B LYS 3.5 14.1 - - - +
86B PHE* 3.9 21.1 - - + -
415B LDA 5.5 0.2 - - + -
416B LDA 4.0 28.9 - - + -
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Residues in contact with THR 55 (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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47B ASP* 5.2 9.5 + - + +
48B THR 3.1 15.9 - - - +
49B GLN* 3.4 36.8 - - - +
50B ILE* 3.8 4.5 - - - -
53B GLN 4.0 1.7 + - - +
54B LEU* 1.3 72.1 - - - +
56B GLY* 1.3 63.4 + - - +
57B PHE* 4.3 0.8 - - - -
84B LEU* 3.4 5.0 - - - +
85B LYS* 2.9 54.7 + - - +
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Residues in contact with GLY 56 (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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316A MET* 3.9 6.7 - - - -
47B ASP* 3.3 4.7 - - - +
48B THR* 2.7 52.4 + - - +
50B ILE* 3.4 6.6 - - - +
55B THR* 1.3 75.8 - - - +
57B PHE* 1.3 60.7 + - - +
83B GLY 3.4 8.1 - - - -
84B LEU* 3.8 11.2 - - - -
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Residues in contact with PHE 57 (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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316A MET* 4.2 2.1 - - - +
350A TYR* 4.0 9.9 - - - +
46B GLY 3.1 12.6 - - - +
47B ASP* 4.4 13.9 - - - +
55B THR* 4.3 2.9 - - - -
56B GLY* 1.3 76.6 - - - +
58B GLY* 1.3 60.4 + - - +
81B TYR* 3.8 30.1 - + - -
82B ALA* 3.3 4.9 - - - +
83B GLY* 2.9 69.7 + - - +
84B LEU* 3.4 18.6 - - - -
85B LYS* 3.9 12.8 - - + -
91B SER* 4.3 12.1 - - - -
92B ILE 3.8 3.1 - - - -
93B ASP* 3.8 21.3 - - + -
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Residues in contact with GLY 58 (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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17A VAL* 4.5 5.2 - - - -
350A TYR* 3.7 25.1 - - - -
45B LYS* 3.3 3.5 - - - +
46B GLY 2.8 32.4 + - - +
57B PHE* 1.3 77.7 - - - +
59B ARG* 1.3 61.1 + - - +
81B TYR* 3.4 12.1 - - - -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.2 7.0 - - - +
14B TYR* 3.0 21.3 + - - -
44B VAL 3.3 11.9 - - - +
45B LYS* 4.0 22.8 - - + +
58B GLY* 1.3 76.3 - - - +
60B PHE* 1.3 67.6 + - - +
61B GLU* 2.7 26.1 + - - -
79B LEU* 3.4 23.4 - - + +
80B ALA* 3.2 6.6 + - - -
81B TYR* 3.0 72.6 + - + +
98B TYR* 6.0 0.6 - - - -
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Residues in contact with PHE 60 (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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17A VAL* 4.6 4.5 - - + +
40A VAL* 3.6 41.5 - - + -
42A LEU* 4.1 16.8 - - + -
62A TRP* 4.0 18.4 - + - -
64A THR* 4.0 13.9 - - + -
66A THR* 4.5 1.3 - - + -
14B TYR* 4.0 1.6 + - - -
42B LEU 5.7 0.7 - - - -
43B GLY* 3.2 4.4 - - - -
44B VAL* 2.8 52.4 + - + +
59B ARG* 1.3 75.8 - - - +
61B GLU* 1.3 71.0 + - - +
62B TRP* 3.9 24.7 - + + -
77B ASN* 3.7 32.1 - - + -
79B LEU 3.2 10.5 - - - -
80B ALA* 4.2 0.4 - - + -
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Residues in contact with GLU 61 (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* 2.6 32.3 + - + +
41B ARG* 4.0 24.1 + - + -
42B LEU 3.6 7.9 - - - +
59B ARG* 2.7 18.2 + - - +
60B PHE* 1.3 77.6 - - - +
62B TRP* 1.3 58.4 - - - +
77B ASN* 3.6 2.4 - - - -
78B ARG* 2.6 70.1 + - + +
79B LEU* 2.8 34.6 + - + +
98B TYR* 5.0 0.7 + - - -
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Residues in contact with TRP 62 (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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62A TRP* 4.4 14.8 - + - -
75A ASN* 5.0 0.8 + - - +
414A CA 4.7 7.2 - - - -
40B VAL* 4.9 2.7 - - + -
41B ARG* 3.2 7.8 - - - +
42B LEU* 2.8 65.1 + - + +
60B PHE* 3.9 21.7 - + + -
61B GLU* 1.3 73.7 - - - +
63B GLU* 1.3 64.5 + - - +
64B THR* 3.5 32.5 - - + -
75B ASN* 3.6 39.2 + - - +
76B LYS 3.3 20.2 - - - -
77B ASN* 3.6 18.5 + - - -
78B ARG* 4.6 0.7 - - - -
60C PHE* 4.0 25.1 - + - -
62C TRP* 4.5 16.8 - + - -
75C ASN* 5.7 0.2 - - - -
77C ASN* 4.6 0.2 - - - -
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Residues in contact with GLU 63 (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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16B LYS* 4.5 1.2 + - - -
39B ARG* 4.0 31.1 + - + +
40B VAL 3.1 17.3 - - - +
41B ARG* 2.8 43.4 + - + +
62B TRP* 1.3 79.6 - - - +
64B THR* 1.3 65.9 + - - +
65B LYS* 5.6 4.3 - - + -
75B ASN* 3.6 0.5 - - - -
76B LYS* 2.7 56.0 + - + +
78B ARG* 3.7 23.9 + - - -
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Residues in contact with THR 64 (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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39B ARG* 3.2 6.7 - - - +
40B VAL* 2.9 38.3 + - + -
62B TRP* 3.5 32.7 - - + -
63B GLU* 1.3 75.9 - - - +
65B LYS* 1.3 62.3 + - - +
66B THR* 3.8 8.4 + - + +
74B GLU 3.3 5.9 + - - -
75B ASN* 3.1 17.6 + - - -
76B LYS* 5.4 0.2 - - - -
60C PHE* 4.1 6.7 - - + -
77C ASN* 2.9 36.1 + - - +
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Residues in contact with LYS 65 (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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37B ASP* 2.9 28.6 + - - +
38B SER 3.7 21.9 + - - -
39B ARG* 3.6 27.1 - - + +
63B GLU* 5.6 4.3 - - + +
64B THR* 1.3 74.6 + - - +
66B THR* 1.3 60.2 + - - +
67B ASN* 3.6 20.1 + - - +
68B LYS* 5.3 2.1 + - + -
69B ALA 5.6 1.0 - - - +
72B GLU* 5.5 5.2 - - + +
74B GLU* 3.1 37.7 + - + +
76B LYS* 3.8 24.0 - - + +
77C ASN* 3.1 19.4 + - - -
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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