Contacts of the strand formed by residues 75 - 93 (chain C) in PDB entry 1ZDH
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C GLN* 3.6 1.7 - - - +
72C VAL* 2.8 34.3 + - + +
73C GLY* 4.1 7.2 - - - +
74C GLY* 1.3 81.1 - - - +
76C GLU* 1.3 66.0 + - - +
77C LEU* 4.0 19.4 + - + +
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C THR* 3.7 19.6 - - + +
70C GLN 3.0 11.2 - - - +
71C THR* 3.8 17.4 + - + +
74C GLY 3.7 5.6 + - - +
75C VAL* 1.3 78.0 - - - +
77C LEU* 1.3 69.9 + - - +
78C PRO* 4.6 2.1 - - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.0 45.3 - - + -
69C THR* 3.5 5.5 - - - +
70C GLN* 2.8 51.4 + - - +
75C VAL* 4.6 18.6 - - + +
76C GLU* 1.3 84.4 - - - +
78C PRO* 1.3 69.7 - - + +
79C VAL* 3.6 6.2 + - + -
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Residues in contact with PRO 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.4 31.8 - - + +
97B THR* 4.8 9.0 - - + -
37C SER* 3.8 13.0 - - - +
39C SER* 2.6 25.3 + - - +
40C GLN* 3.6 25.1 - - + +
68C ALA 3.9 2.0 - - - +
69C THR* 4.7 3.4 - - - +
76C GLU 4.6 1.1 - - - +
77C LEU* 1.3 87.3 - - + +
79C VAL* 1.3 59.2 + - - +
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.3 10.8 - - + -
39C SER* 4.2 5.8 - - - -
40C GLN* 3.0 16.7 + - - +
67C VAL* 3.9 0.3 - - - -
68C ALA* 2.8 43.3 + - + +
69C THR 4.1 0.9 - - - -
70C GLN* 3.8 46.4 - - + +
77C LEU* 4.0 10.5 - - + +
78C PRO* 1.3 79.1 - - - +
80C ALA* 1.3 70.9 + - - +
81C ALA* 4.4 2.2 - - - +
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER 3.5 19.8 + - - +
40C GLN* 4.7 0.7 - - - -
65C PRO* 3.9 19.1 - - + -
66C LYS 3.2 6.5 - - - -
67C VAL* 4.5 0.4 - - - +
79C VAL* 1.3 78.5 - - - +
81C ALA* 1.3 67.1 + - - +
82C TRP* 3.9 15.8 - - - +
83C ARG* 4.1 11.9 - - + +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LYS* 2.6 23.8 + - + +
68C ALA* 3.8 20.3 - - + +
79C VAL* 3.9 4.7 - - - -
80C ALA* 1.3 73.4 - - - +
82C TRP* 1.3 75.2 + - + +
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Residues in contact with TRP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C VAL* 4.8 3.1 - - + -
65C PRO* 3.6 0.8 - - - +
66C LYS* 2.9 66.7 + - + +
80C ALA* 3.1 5.7 - - - +
81C ALA* 1.3 87.5 - - + +
83C ARG* 1.3 81.9 + - - +
84C SER* 4.0 17.9 - - - -
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Residues in contact with ARG 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.9 14.9 + - - +
39C SER* 3.1 26.1 + - - +
40C GLN 4.0 1.8 - - - -
41C ALA 2.8 34.1 + - - +
43C LYS 4.8 1.0 - - - +
63C GLU* 2.9 43.2 + - - +
64C VAL 3.3 7.4 - - - +
65C PRO* 3.9 16.1 - - + +
80C ALA* 4.1 8.0 - - + +
82C TRP* 1.3 92.5 - - - +
84C SER* 1.3 63.2 + - - +
85C TYR* 3.4 41.1 - - + +
10S U 6.2 0.6 - - - -
11S C 4.1 6.9 + - - -
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Residues in contact with SER 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C VAL 3.7 0.5 - - - +
63C GLU* 3.4 8.1 - - - +
64C VAL* 3.1 41.4 + - - +
82C TRP* 4.0 14.2 - - - -
83C ARG* 1.3 74.9 - - - +
85C TYR* 1.3 63.5 + - - +
86C LEU 5.4 0.2 - - - -
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Residues in contact with TYR 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL 3.7 2.5 - - - +
63C GLU* 3.8 20.2 - - + -
83C ARG* 3.4 36.0 - - + +
84C SER* 1.3 76.4 - - - +
86C LEU* 1.3 61.4 + - - +
87C ASN* 3.9 6.5 + - - +
10S U 3.1 27.8 - - - -
11S C 2.6 109.2 + + + +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 6.0 0.2 - - + -
61C LYS* 3.3 6.6 - - - +
62C VAL* 2.9 58.0 + - + +
84C SER* 4.1 0.8 - - - -
85C TYR* 1.3 73.2 - - - +
87C ASN* 1.3 72.8 + - - +
88C MET* 4.1 29.4 - - + -
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Residues in contact with ASN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE 3.7 2.9 - - - -
61C LYS* 3.2 38.2 + - + +
85C TYR* 3.9 8.7 + - - +
86C LEU* 1.3 83.3 - - - +
88C MET* 1.3 61.4 + - - +
89C GLU* 5.6 1.6 - - + -
9S A 4.0 11.0 - - - +
11S C 3.0 32.9 + - - +
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Residues in contact with MET 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C TYR 3.8 0.2 - - - +
59C THR* 3.5 4.2 - - - +
60C ILE* 2.9 65.3 + - + +
86C LEU* 4.1 28.9 - - + -
87C ASN* 1.3 75.3 - - - +
89C GLU* 1.3 66.1 + - - +
90C LEU* 4.3 8.3 - - + -
108C MET* 4.2 24.9 - - - -
112C LEU* 6.2 4.0 - - - -
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Residues in contact with GLU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 3.6 14.0 + - - -
57C LYS* 3.8 24.6 + - - -
58C TYR 3.2 9.2 - - - +
59C THR* 3.3 26.3 + - + +
87C ASN* 5.6 1.6 - - + -
88C MET* 1.3 80.4 - - - +
90C LEU* 1.3 62.0 + - - +
91C THR* 4.1 2.1 + - - +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ARG 3.8 1.0 - - - +
57C LYS* 3.3 4.3 - - - -
58C TYR* 2.9 50.0 + - + -
60C ILE* 6.1 2.2 - - + +
88C MET* 4.3 7.4 - - + -
89C GLU* 1.3 75.4 - - - +
91C THR* 1.3 67.5 + - - +
92C ILE* 3.9 19.8 + - + -
104C ILE* 4.0 21.8 - - + -
105C VAL* 6.2 0.2 - - + -
108C MET* 3.6 36.6 - - + -
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Residues in contact with THR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C SER* 4.7 2.9 - - - +
55C ASN* 3.5 39.9 - - + +
56C ARG 3.6 4.3 - - - +
57C LYS* 3.8 24.4 + - - +
89C GLU* 4.1 2.8 + - - +
90C LEU* 1.3 76.3 - - - +
92C ILE* 1.3 66.4 + - - +
93C PRO* 4.2 5.2 - - + +
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASN* 4.1 2.0 - - - -
56C ARG* 2.9 46.5 + - - +
58C TYR* 4.3 17.3 - - + -
90C LEU* 3.9 31.4 + - + +
91C THR* 1.3 79.5 - - - +
93C PRO* 1.4 78.5 - - + +
94C ILE 3.7 0.2 + - - -
96C ALA* 3.7 19.1 - - + -
101C CYS* 4.2 16.2 - - + -
104C ILE* 3.9 29.8 - - + -
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Residues in contact with PRO 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLN* 3.1 12.1 - - + +
55C ASN* 3.5 11.9 - - - +
91C THR* 4.2 5.6 - - + +
92C ILE* 1.4 93.5 - - + +
94C ILE* 1.3 59.1 + - - +
95C PHE* 3.0 28.7 + - + +
96C ALA* 3.2 21.3 + - + +
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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