Contacts of the strand formed by residues 55 - 72 (chain A) in PDB entry 1ZDJ
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 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 3.4 6.4 - - - +
51A SER* 3.2 34.4 + - - +
52A SER* 3.2 25.8 + - - +
53A ALA 3.7 0.2 - - - -
54A GLN* 1.3 88.8 + - - +
56A ARG* 1.3 65.5 - - - +
91A THR* 3.6 26.1 - - + +
92A ILE 3.4 3.8 - - - -
93A PRO* 3.8 15.6 - - - +
94A ILE* 4.1 1.1 - - - +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.5 18.8 - - + +
49A ARG 3.2 9.8 - - - +
50A GLN* 3.6 24.9 - - - +
51A SER* 4.4 0.2 - - - -
55A ASN* 1.3 79.1 - - - +
57A LYS* 1.3 61.2 + - - +
58A TYR* 2.7 41.2 + - + -
90A LEU 3.7 0.5 - - - +
91A THR* 3.4 3.6 - - - +
92A ILE* 2.9 45.8 + - + +
93A PRO 5.7 1.6 + - - -
94A ILE* 4.5 8.3 - - + +
101A CYS* 5.5 5.9 - - - -
38B ARG* 3.4 55.4 - - - +
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 3.7 1.0 - - - +
48A VAL* 3.3 2.5 - - - -
49A ARG* 2.8 73.5 + - - +
51A SER* 3.6 18.8 - - - +
56A ARG* 1.3 76.5 - - - +
58A TYR* 1.3 70.3 + - - +
59A THR* 4.6 4.3 + - - +
89A GLU* 3.1 47.2 + - - -
90A LEU 3.3 6.7 - - - +
91A THR* 3.8 17.9 - - - +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A CYS* 4.9 10.5 - - - -
47A SER 3.2 6.1 - - - +
48A VAL* 3.5 27.6 - - + -
56A ARG* 2.7 37.8 + - + -
57A LYS* 1.3 77.2 - - - +
59A THR* 1.3 61.5 + - - +
60A ILE* 4.1 18.9 - - + +
88A MET 3.7 0.3 - - - +
89A GLU* 3.3 6.6 - - - +
90A LEU* 2.9 47.7 + - + +
92A ILE* 3.8 30.3 - - + -
101A CYS* 6.2 0.2 - - - -
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A CYS* 3.3 1.0 - - - -
47A SER* 2.8 27.5 + - - -
49A ARG* 4.5 13.9 + - - -
57A LYS* 4.6 5.0 + - - +
58A TYR* 1.3 74.6 + - - +
60A ILE* 1.3 62.7 + - - +
61A LYS* 4.1 22.0 - - + -
87A ASN* 5.3 1.8 - - - +
88A MET 3.5 7.4 - - - +
89A GLU* 4.1 20.4 + - + +
12R A 2.9 43.0 + - + +
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Residues in contact with ILE 60 (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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44A VAL* 4.9 7.6 - - + -
45A THR 3.3 9.0 - - - +
46A CYS* 4.3 17.7 - - + -
58A TYR* 4.4 17.7 - - + -
59A THR* 1.3 82.4 - - - +
61A LYS* 1.3 69.2 + - - +
62A VAL* 4.8 10.1 - - + -
86A LEU* 3.8 1.6 - - + +
87A ASN* 3.7 0.7 - - - -
88A MET* 2.8 65.4 + - + +
90A LEU* 5.6 8.5 - - + -
108A MET* 6.4 2.2 - - + -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS 3.9 0.6 - - - +
44A VAL* 3.3 4.5 - - - +
45A THR* 2.9 42.4 + - - +
59A THR* 4.1 15.0 - - + -
60A ILE* 1.3 75.9 - - - +
62A VAL* 1.3 65.4 + - - +
63A GLU* 5.8 3.4 - - + -
86A LEU 3.2 8.3 - - - +
87A ASN* 3.2 31.6 - - - +
9R A 5.7 1.6 + - - +
11R C 4.7 17.5 + - - +
12R A 3.1 62.4 + - + +
13R C 4.3 14.8 - - - +
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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
----------------------------------------------------------
9A LEU* 4.3 25.1 - - + -
43A LYS 3.3 9.0 - - - +
44A VAL* 4.2 17.3 - - + -
60A ILE* 4.8 8.1 - - + -
61A LYS* 1.3 78.8 - - - +
63A GLU* 1.3 65.3 + - - +
64A VAL* 4.1 20.6 - - + -
84A SER 3.7 0.7 - - - +
85A TYR* 3.5 3.8 - - - +
86A LEU* 2.9 57.2 + - + +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 3.5 11.1 - - - +
43A LYS* 2.9 57.2 + - + +
61A LYS* 5.8 3.4 - - + -
62A VAL* 1.3 76.3 - - - +
64A VAL* 1.3 63.8 + - - +
65A PRO* 3.6 0.8 - - - +
83A ARG* 2.8 35.3 + - - +
84A SER 3.3 4.7 - - - +
85A TYR* 3.7 28.0 - - + -
11R C 3.1 32.3 + - - +
12R A 4.2 0.7 + - - -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.3 1.8 - - + -
10A VAL* 6.1 1.3 - - + -
42A TYR* 4.0 25.1 - - + +
62A VAL* 4.2 17.3 - - + -
63A GLU* 1.3 76.1 - - - +
65A PRO* 1.3 69.1 - - + +
66A LYS 4.1 0.2 + - - -
82A TRP* 4.7 4.9 - - + -
83A ARG* 3.5 3.2 - - - -
84A SER* 2.9 48.1 + - - +
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Residues in contact with PRO 65 (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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40A GLN 3.4 22.9 - - - +
41A ALA 3.8 4.3 - - - +
42A TYR* 3.7 35.9 + - + -
63A GLU 3.6 9.2 - - - +
64A VAL* 1.3 90.0 - - - +
66A LYS* 1.3 61.6 + - - +
67A VAL* 3.7 9.5 + - + +
80A ALA* 4.0 11.9 - - + -
82A TRP* 3.6 6.3 - - - +
83A ARG* 3.8 25.1 - - + +
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Residues in contact with LYS 66 (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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65A PRO* 1.3 71.3 - - - +
67A VAL* 1.3 60.1 + - - +
80A ALA* 3.3 1.1 - - - -
81A ALA* 2.6 42.4 + - + -
82A TRP* 3.0 64.8 + - + +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN* 5.4 3.6 - - - +
40A GLN* 3.5 53.2 - - + +
42A TYR* 6.3 0.9 - - + -
65A PRO* 3.7 12.0 + - + +
66A LYS* 1.3 83.7 - - - +
68A ALA* 1.3 61.2 + - - +
79A VAL 3.5 4.0 - - - +
80A ALA* 4.1 0.2 - - - +
81A ALA* 5.0 0.2 - - - +
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Residues in contact with ALA 68 (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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40A GLN* 3.0 8.6 + - - -
66A LYS 3.8 0.2 + - - -
67A VAL* 1.3 75.8 - - - +
69A THR* 1.3 66.8 + - - +
70A GLN* 5.7 0.4 - - + -
79A VAL* 2.8 44.2 + - + +
81A ALA* 3.9 20.0 - - + -
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Residues in contact with THR 69 (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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40A GLN* 5.2 1.6 + - - -
68A ALA* 1.3 78.7 + - - +
70A GLN* 1.3 61.1 + - - +
71A THR* 3.9 3.6 + - - -
76A GLU* 3.9 36.3 - - + +
77A LEU 3.4 16.8 - - - +
78A PRO* 4.8 2.5 - - + +
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Residues in contact with GLN 70 (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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68A ALA* 5.8 0.2 - - + -
69A THR* 1.3 75.1 - - - +
71A THR* 1.3 67.0 + - - +
72A VAL* 3.5 24.5 + - + +
76A GLU* 4.4 1.3 - - - -
77A LEU* 2.9 34.0 + - - +
79A VAL* 3.8 32.6 - - + +
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Residues in contact with THR 71 (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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69A THR 3.9 3.4 + - - -
70A GLN* 1.3 76.5 + - - +
72A VAL* 1.3 60.9 + - - +
73A GLY 4.0 0.9 + - - -
74A GLY* 3.8 14.8 + - - +
75A VAL 3.2 24.9 - - - +
76A GLU* 4.1 14.8 + - + +
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Residues in contact with VAL 72 (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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70A GLN* 3.5 28.9 + - + +
71A THR* 1.3 73.5 - - - +
73A GLY* 1.3 70.8 + - - +
74A GLY 3.1 0.9 - - - -
75A VAL* 2.8 26.9 + - - +
77A LEU* 3.8 28.4 - - + +
79A VAL* 6.1 1.3 - - + -
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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