Contacts of the strand formed by residues 75 - 93 (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 VAL 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 3.2 3.8 - - - +
72A VAL 2.8 38.2 + - - +
73A GLY 3.8 9.0 - - - +
74A GLY* 1.3 86.7 - - - +
76A GLU* 1.3 75.1 + - - +
77A LEU* 3.7 14.1 + - + +
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Residues in contact with GLU 76 (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 22.2 - - + +
70A GLN 3.6 4.9 - - - -
71A THR* 4.1 16.3 + - + +
75A VAL* 1.3 80.9 - - - +
77A LEU* 1.3 66.1 + - - +
78A PRO* 4.5 2.1 - - - +
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Residues in contact with LEU 77 (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* 3.4 6.4 - - - -
70A GLN 2.9 34.7 + - - +
72A VAL* 3.8 31.4 - - + +
75A VAL* 4.3 17.3 - - + +
76A GLU* 1.3 81.3 - - - +
78A PRO* 1.4 71.7 - - + +
79A VAL* 3.8 4.4 - - + +
54C GLN* 5.8 0.7 - - - +
95C PHE* 4.0 46.9 - - + -
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Residues in contact with PRO 78 (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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37A SER* 4.0 10.5 - - - +
39A SER* 2.9 18.4 + - - -
40A GLN* 3.7 25.1 - - - +
68A ALA 3.9 2.0 - - - +
69A THR* 4.8 4.0 - - + +
76A GLU 4.5 2.2 - - - +
77A LEU* 1.4 86.8 - - + +
79A VAL* 1.3 59.0 + - - +
95C PHE* 3.4 47.2 - - + +
97C THR* 5.4 6.1 - - + -
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Residues in contact with VAL 79 (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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39A SER* 4.3 5.2 - - - +
40A GLN* 2.9 16.9 + - - +
67A VAL* 3.5 0.7 - - - -
68A ALA* 2.8 51.4 + - + +
70A GLN* 3.8 33.2 - - + +
72A VAL* 6.1 1.6 - - + -
77A LEU* 3.8 9.4 - - + +
78A PRO* 1.3 79.2 - - - +
80A ALA* 1.3 69.4 + - - +
81A ALA* 4.2 1.6 - - - +
95C PHE* 4.7 12.3 - - + -
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Residues in contact with ALA 80 (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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39A SER* 3.5 20.7 + - - +
40A GLN* 4.7 1.6 - - - -
65A PRO* 4.0 22.2 - - + -
66A LYS 3.4 8.3 - - - +
67A VAL* 4.1 1.1 - - - +
79A VAL* 1.3 82.4 - - - +
81A ALA* 1.3 65.3 + - - +
82A TRP* 3.1 8.0 + - - +
83A ARG* 4.1 10.5 - - - +
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Residues in contact with ALA 81 (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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66A LYS* 2.6 23.6 + - + +
67A VAL 4.9 0.4 - - - +
68A ALA* 3.9 22.9 - - + +
79A VAL* 4.8 1.8 - - - -
80A ALA* 1.3 71.9 - - - +
82A TRP* 1.3 74.4 + - + +
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Residues in contact with TRP 82 (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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64A VAL* 4.7 6.1 - - + -
65A PRO* 3.6 0.6 - - - +
66A LYS* 3.0 68.4 + - + +
80A ALA* 3.1 5.6 - - - +
81A ALA* 1.3 89.2 - - + +
83A ARG* 1.3 77.1 + - - +
84A SER* 4.5 17.5 - - - -
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Residues in contact with ARG 83 (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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38A ARG 4.2 4.9 + - - -
39A SER 3.2 25.3 + - - -
41A ALA 2.8 35.7 + - - +
43A LYS* 5.0 1.8 - - - +
63A GLU* 2.8 46.9 + - + +
64A VAL 3.5 4.3 - - - +
65A PRO* 3.8 21.4 - - + +
80A ALA* 4.1 10.3 - - + +
82A TRP* 1.3 87.5 - - - +
84A SER* 1.3 60.4 + - - +
85A TYR* 3.4 41.6 - - + +
10R U 5.3 2.8 + - - +
11R C 4.2 5.2 - - - -
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Residues in contact with SER 84 (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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62A VAL 3.7 0.7 - - - +
63A GLU* 3.3 5.7 - - - +
64A VAL* 2.9 50.4 + - - +
82A TRP* 4.3 13.6 - - - -
83A ARG* 1.3 75.0 - - - +
85A TYR* 1.3 61.2 + - - +
86A LEU 4.3 0.2 - - - -
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Residues in contact with TYR 85 (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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62A VAL 3.5 3.1 - - - +
63A GLU* 3.7 21.8 - - + -
83A ARG* 3.4 35.4 - - + +
84A SER* 1.3 76.4 + - - +
86A LEU* 1.3 60.0 + - - +
87A ASN* 4.1 6.6 + - - +
10R U 3.1 27.8 - - - -
11R C 2.5 106.8 + + + +
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Residues in contact with LEU 86 (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 ILE* 5.5 1.6 - - + +
61A LYS* 3.2 7.1 - - - +
62A VAL* 2.9 56.5 + - + +
84A SER 4.3 0.4 + - - -
85A TYR* 1.3 72.8 - - - +
87A ASN* 1.3 76.7 + - - +
88A MET* 3.5 35.7 - - + +
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Residues in contact with ASN 87 (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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59A THR* 5.3 1.9 - - - +
60A ILE 3.7 1.8 - - - -
61A LYS* 3.2 36.9 - - - +
85A TYR* 4.1 10.3 + - - +
86A LEU* 1.3 88.0 + - - +
88A MET* 1.3 61.6 + - - +
89A GLU* 5.4 2.8 - - + +
9R A 4.7 8.4 + - - +
11R C 3.2 26.5 + - - +
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Residues in contact with MET 88 (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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58A TYR 3.7 0.6 - - - +
59A THR* 3.5 5.1 - - - +
60A ILE* 2.8 74.6 + - + +
86A LEU* 3.5 34.1 - - + -
87A ASN* 1.3 74.8 + - - +
89A GLU* 1.3 65.0 + - - +
90A LEU* 4.2 2.7 - - + -
108A MET* 5.1 16.2 - - - +
112A LEU* 5.8 7.9 - - + -
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Residues in contact with GLU 89 (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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49A ARG* 5.5 0.2 + - - -
57A LYS* 3.1 41.4 + - - -
58A TYR 3.3 6.3 - - - +
59A THR* 4.1 16.6 + - + +
87A ASN* 5.4 2.2 - - + +
88A MET* 1.3 81.4 - - - +
90A LEU* 1.3 60.5 + - - +
91A THR* 4.1 2.1 + - - +
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Residues in contact with LEU 90 (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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56A ARG 3.7 0.7 - - - +
57A LYS* 3.3 3.7 - - - -
58A TYR* 2.9 49.2 + - + +
60A ILE* 5.6 7.8 - - + +
88A MET* 4.2 2.4 - - + -
89A GLU* 1.3 73.4 - - - +
91A THR* 1.3 63.5 - - - +
92A ILE* 3.7 30.8 + - + -
104A ILE* 3.7 30.5 - - + -
108A MET* 4.6 21.8 - - + -
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Residues in contact with THR 91 (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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51A SER* 4.7 3.1 + - - +
55A ASN* 3.6 38.8 - - + +
56A ARG 3.4 4.0 - - - +
57A LYS* 3.8 20.8 - - - +
89A GLU* 4.1 2.5 + - - +
90A LEU* 1.3 77.4 - - - +
92A ILE* 1.3 64.0 + - - +
93A PRO* 4.2 4.2 - - + +
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Residues in contact with ILE 92 (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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55A ASN* 3.4 3.1 - - - -
56A ARG* 2.9 44.2 + - - +
58A TYR* 3.8 22.4 - - + -
90A LEU* 3.7 32.8 - - + +
91A THR* 1.3 77.7 - - - +
93A PRO* 1.4 80.0 - - + +
96A ALA* 3.8 16.8 - - + -
101A CYS* 4.2 16.8 - - + -
104A ILE* 4.0 27.4 - - + -
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Residues in contact with PRO 93 (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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54A GLN 3.4 10.5 - - - +
55A ASN* 3.8 10.3 - - - +
56A ARG* 5.7 2.4 + - - +
91A THR* 4.2 4.5 - - + +
92A ILE* 1.4 101.0 - - + +
94A ILE* 1.3 61.8 + - - +
95A PHE* 3.0 21.3 + - + +
96A ALA* 3.5 20.0 + - + +
104A ILE* 6.1 0.4 - - + -
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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