Contacts of the strand formed by residues 48 - 65 (chain A) in PDB entry 4ZR2
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 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASP 3.9 0.9 - - - +
44A GLN* 3.3 6.6 - - - +
45A ASP* 2.9 44.2 + - + +
47A ASP* 1.3 78.5 - - - +
49A PHE* 1.3 61.3 + - - +
50A LYS* 2.7 34.8 + - - +
63B ASP* 3.1 25.6 + - - -
64B PHE 3.6 3.1 + - - -
65B THR* 3.2 20.9 + - + +
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.9 12.8 - - + -
42A ILE* 4.1 12.6 - - + -
43A ASP 3.8 2.2 - - - -
44A GLN* 3.3 47.3 - - + -
47A ASP* 3.7 13.0 - - - -
48A ASN* 1.3 77.2 - - - +
50A LYS* 1.3 63.2 + - - +
51A THR* 4.1 6.5 - - + -
62B VAL 3.7 0.9 - - - +
63B ASP* 3.4 4.2 - - - +
64B PHE* 2.8 73.6 + + + -
66B VAL* 3.7 23.8 - - + -
88B TRP* 3.8 11.9 - + - -
93B LEU* 3.7 24.0 - - + -
108B LYS* 5.8 1.3 - - - -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 3.8 0.7 - - - +
42A ILE* 3.6 0.3 - - - -
43A ASP* 2.8 57.6 + - + +
48A ASN* 2.7 29.9 + - - +
49A PHE* 1.3 77.4 - - - +
51A THR* 1.3 62.7 + - - +
61B ASP* 6.5 0.4 - - + -
62B VAL 3.2 6.3 - - - +
63B ASP* 3.5 28.0 + - + -
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.2 12.5 - - - +
41A VAL 3.2 7.9 - - - -
42A ILE* 3.9 25.6 - - + -
49A PHE* 4.4 11.9 - - + -
50A LYS* 1.3 82.5 - - - +
52A LYS* 1.3 63.1 + - - +
60B TRP 4.4 0.7 - - - +
61B ASP* 3.5 4.2 - - - +
62B VAL* 2.9 47.9 + - - +
64B PHE* 4.6 8.6 - - + -
108B LYS* 4.5 12.9 + - - +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 3.8 0.9 - - - +
40A LEU* 3.6 3.0 - - - -
41A VAL* 2.8 41.9 + - + +
51A THR* 1.3 76.8 - - - +
53A THR* 1.3 64.5 + - - +
54A THR* 4.2 20.9 - - + +
58B ARG* 4.3 30.6 + - - +
59B ASN 2.9 29.6 + - - +
60B TRP* 4.8 2.4 - - - +
61B ASP* 2.9 44.7 + - - +
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 3.4 32.9 + - + +
39A THR 3.4 10.1 - - - +
40A LEU* 3.6 17.6 - - + +
52A LYS* 1.3 73.5 - - - +
54A THR* 1.3 77.1 + - - +
59B ASN* 2.9 56.5 + - - +
60B TRP 5.4 0.4 + - - -
130B PHE* 6.4 0.2 - - + -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 3.4 1.9 - - - -
39A THR* 2.8 49.0 + - - +
41A VAL* 6.0 2.7 - - + +
52A LYS* 4.2 16.6 - - + -
53A THR* 1.3 83.1 - - - +
55A SER* 1.3 64.7 + - - +
56B THR* 5.6 3.4 - - - -
57B PHE 3.0 8.7 - - - -
58B ARG* 3.7 26.2 - - + +
59B ASN* 5.5 0.2 - - - -
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.4 34.5 - - - +
37A THR 3.1 27.1 - - - -
38A GLN* 4.0 7.1 - - - +
39A THR* 5.8 0.4 - - - -
54A THR* 1.3 76.4 - - - +
56A THR* 1.3 59.8 + - - +
56B THR* 3.4 4.8 - - - -
57B PHE* 2.8 50.2 + - - +
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.6 15.5 - - - +
37A THR 4.1 6.6 + - - -
55A SER* 1.3 73.9 - - - +
57A PHE* 1.3 70.4 + - - +
58A ARG 4.3 2.5 - - - +
59A ASN* 4.5 22.0 - - - +
54B THR* 4.9 4.3 - - - -
55B SER 3.8 10.1 - - - +
56B THR* 4.2 13.3 - - + +
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.8 37.5 - - + -
36A LEU* 3.9 12.0 - - + +
55A SER 3.5 1.6 + - - -
56A THR* 1.3 75.4 - - - +
58A ARG* 1.3 101.6 + - + +
59A ASN* 5.6 0.2 + - - -
60A TRP* 4.9 5.2 - + - -
32B ILE* 5.8 0.9 - - + -
33B ALA* 6.3 0.4 - - + -
36B LEU* 3.8 27.1 - - + -
55B SER* 2.8 31.1 + - - +
57B PHE* 3.6 27.1 - + + -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 4.3 1.1 - - - +
57A PHE* 1.3 123.3 - - + +
59A ASN* 1.3 67.4 + - - +
60A TRP* 3.5 36.1 - - + +
53B THR 3.7 1.1 - - - +
54B THR* 3.3 3.1 - - - -
55B SER* 2.8 32.5 + - - +
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 4.5 13.4 - - - +
58A ARG* 1.3 76.8 - - - +
60A TRP* 1.3 72.7 + - - +
61A ASP* 4.9 1.5 - - - +
52B LYS* 4.6 19.5 - - + +
53B THR 3.3 6.1 - - - +
54B THR* 3.0 31.2 - - + +
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.9 6.7 - + - -
58A ARG* 3.5 37.9 - - + +
59A ASN* 1.3 79.3 - - - +
61A ASP* 1.3 67.0 + - - +
62A VAL* 4.2 2.4 + - + +
75A LYS* 3.6 20.3 + - + +
76A SER* 3.8 37.5 - - - +
36B LEU* 5.3 3.8 - - + -
38B GLN* 4.0 13.0 - - - -
52B LYS* 3.4 2.4 - - - -
53B THR* 2.8 61.5 + - + -
55B SER* 3.4 33.0 - - - -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 4.9 1.7 - - - +
60A TRP* 1.3 81.2 + - - +
62A VAL* 1.3 63.0 + - - +
63A ASP* 4.4 9.1 - - - +
51B THR 3.3 8.6 - - - +
52B LYS* 2.7 46.0 + - - +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TRP* 5.4 2.5 - - + +
61A ASP* 1.3 75.9 - - - +
63A ASP* 1.3 67.5 + - - +
64A PHE* 4.1 20.1 - - + -
70A PHE* 4.1 17.7 - - + -
72A GLU* 4.1 23.3 - - + +
106A TRP* 6.4 1.6 - - + -
201A RET 3.8 20.9 - - + -
51B THR* 2.8 55.2 + - - +
53B THR* 5.6 1.1 - - - +
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 4.4 7.7 - - - +
62A VAL* 1.3 87.2 + - - +
64A PHE* 1.3 66.2 + - - +
70A PHE* 4.2 14.2 - - - +
49B PHE 3.2 10.3 - - - +
50B LYS* 3.4 32.8 - - + +
51B THR 3.6 5.2 + - - +
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.1 26.0 - - + -
63A ASP* 1.3 79.0 - - - +
65A THR* 1.3 68.0 + - - +
66A VAL* 4.5 0.7 - - + -
70A PHE* 3.5 31.0 - + + -
86A VAL* 3.9 30.3 - - + -
93A LEU* 4.1 14.1 - - + -
106A TRP* 4.2 20.6 - + - -
108A LYS* 5.5 0.9 - - - -
201A RET 5.5 1.3 - - + -
48B ASN* 3.7 1.7 - - - +
49B PHE* 2.7 77.7 + + + +
51B THR* 4.5 9.2 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 1.3 79.9 - - - +
66A VAL* 1.3 78.8 + - - +
67A GLY 3.3 0.3 + - - -
68A VAL* 3.1 42.6 + - + +
70A PHE* 5.5 0.4 - - - -
86A VAL* 5.2 1.9 + - - +
47B ASP* 3.3 13.7 - - + +
48B ASN* 2.7 27.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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