Contacts of the strand formed by residues 88 - 96 (chain C) in PDB entry 3ZXR
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 THR 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.3 4.7 - - - -
20C TYR* 3.2 20.4 - - + +
22C ASP* 3.8 30.7 - - + +
80C ILE* 3.5 8.4 - - - +
81C ASP* 2.9 33.9 + - - +
84C ARG* 3.2 37.4 + - - +
86C ALA 2.7 21.2 + - - -
87C LYS* 1.3 76.5 + - - +
89C LEU* 1.3 63.6 + - - +
90C ASN* 3.9 4.7 - - - +
200D ASP* 4.3 0.7 + - - -
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Residues in contact with LEU 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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9C VAL* 3.8 28.7 - - + +
12C LEU* 3.9 19.3 - - + -
13C ALA* 4.2 22.7 - - + -
18C VAL* 3.9 18.8 - - + +
20C TYR 2.9 8.4 + - - +
21C VAL* 3.3 10.1 - - + +
22C ASP 2.8 30.2 + - - +
42C PHE* 4.3 4.9 - - + -
78C ALA* 4.1 2.2 - - + -
79C ARG 3.4 30.3 - - - +
80C ILE* 3.7 13.5 - - + -
88C THR* 1.3 73.4 - - - +
90C ASN* 1.3 56.8 + - - +
91C ILE* 3.9 16.2 - - + -
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Residues in contact with ASN 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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22C ASP* 3.2 24.4 - - - +
24C ARG* 3.7 32.1 - - - +
77C THR 3.5 2.9 - - - +
78C ALA* 3.2 5.2 - - - -
79C ARG* 2.7 42.9 + - + +
80C ILE 4.9 0.6 - - - -
81C ASP* 3.0 43.7 + - - +
82C PRO* 5.1 0.6 - - - +
84C ARG* 4.9 0.3 + - - -
88C THR* 3.9 2.1 - - - +
89C LEU* 1.3 74.1 - - - +
91C ILE* 1.3 60.3 + - - +
92C ASN* 5.6 0.9 - - - +
244C LEU* 5.0 9.4 - - + +
247C TYR* 4.1 5.3 - - - -
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Residues in contact with ILE 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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9C VAL* 3.8 13.7 - - + -
21C VAL* 3.9 15.3 - - + -
22C ASP 3.0 9.3 + - - +
24C ARG* 2.9 26.0 + - - +
42C PHE* 3.4 37.5 - - + -
47C PHE* 5.6 0.9 - - + -
73C PRO* 4.3 6.1 - - + -
74C ASP 3.8 15.3 - - - +
75C PRO* 4.8 2.0 - - + -
77C THR* 3.8 11.2 - - - +
78C ALA* 4.0 14.8 - - + +
89C LEU* 3.9 7.6 - - + -
90C ASN* 1.3 81.0 - - - +
92C ASN* 1.3 75.7 + - - +
93C PHE* 3.3 20.6 - - + -
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Residues in contact with ASN 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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24C ARG* 3.2 23.6 - - - +
32C MET* 3.8 15.7 - - - +
74C ASP* 2.8 32.5 + - - +
77C THR* 2.8 32.1 + - + +
90C ASN* 5.6 1.0 - - - +
91C ILE* 1.3 74.4 + - - +
93C PHE* 1.3 57.1 + - - +
109C ARG* 4.0 12.7 - - - +
240C ASP* 3.0 34.8 + - - +
243C GLN* 5.6 1.6 - - - +
377C TYR* 3.8 7.3 + - - -
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Residues in contact with PHE 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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21C VAL* 5.6 1.1 - - + -
22C ASP 5.5 0.2 - - - -
23C VAL* 3.7 38.8 - - + -
24C ARG 2.6 14.0 + - - +
25C PHE* 4.0 10.8 - - - +
42C PHE* 5.5 1.3 - + - -
46C VAL* 4.1 18.6 - - + -
51C LEU* 4.1 7.2 - - + -
71C LEU* 3.6 28.5 - - + -
72C LEU 3.4 14.1 - - - +
73C PRO* 3.3 40.4 - - + -
74C ASP 4.3 0.2 - - - +
91C ILE* 3.3 37.0 - - + -
92C ASN* 1.3 79.5 - - - +
94C PHE* 1.3 60.8 + - - +
95C VAL 4.2 0.2 + - - -
107C ASP* 4.4 1.6 - - - +
109C ARG* 3.2 26.3 + - - -
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Residues in contact with PHE 94 (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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71C LEU* 3.2 7.1 - - - -
72C LEU* 2.8 39.1 + - + +
73C PRO 4.6 2.9 - - - -
74C ASP* 3.4 33.2 - - + -
93C PHE* 1.3 73.4 - - - +
95C VAL* 1.3 62.0 + - - +
96C HIS* 3.5 20.5 - - - +
107C ASP* 3.3 11.4 - - - +
109C ARG* 3.4 46.7 - - + -
113C ARG* 3.2 52.9 - - + +
236C LEU* 4.4 8.5 - - + -
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Residues in contact with VAL 95 (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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25C PHE* 4.2 11.0 - - + -
26C CYS 5.1 0.2 - - - +
53C PHE* 3.9 15.3 - - + -
61C PHE* 3.9 21.8 - - + -
69C MET* 3.7 15.3 - - + -
70C LEU 3.4 9.4 - - - +
71C LEU* 3.8 17.3 - - + -
94C PHE* 1.3 73.3 - - - +
96C HIS* 1.3 66.2 + - - +
103C PRO* 3.8 1.7 - - - +
104C TYR* 2.9 44.2 + - + +
107C ASP* 2.7 35.8 + - + +
113C ARG* 5.3 0.2 + - - -
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Residues in contact with HIS 96 (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 MET* 3.5 11.0 - - - +
70C LEU* 2.7 47.6 + - + +
72C LEU* 3.6 30.5 - - + +
94C PHE* 3.5 31.0 - - + +
95C VAL* 1.3 81.4 - - - +
97C ASP* 1.3 67.6 + - - +
101C LEU 2.8 26.7 + - - +
102C GLU 3.3 5.6 - - - +
103C PRO* 3.5 26.1 - - + -
104C TYR 4.1 0.9 - - - +
113C ARG* 3.9 9.1 + - - -
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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