Contacts of the strand formed by residues 88 - 96 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D VAL* 4.3 4.7 - - - -
20D TYR* 3.3 20.0 - - + +
22D ASP* 3.9 10.5 - - + +
80D ILE* 3.5 7.6 - - - +
81D ASP* 2.8 38.8 + - - +
84D ARG* 3.2 47.3 + - - +
86D ALA 2.6 21.6 + - - -
87D LYS* 1.3 76.2 + - - +
89D LEU* 1.3 58.7 + - - +
90D ASN* 3.8 15.5 - - - +
200E ASP* 4.4 0.7 + - - -
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.7 29.8 - - + +
12D LEU* 3.8 20.0 - - + -
13D ALA* 4.2 20.4 - - + -
18D VAL* 3.9 19.4 - - + +
20D TYR 2.9 7.6 + - - +
21D VAL* 3.3 10.6 - - + +
22D ASP 2.9 23.6 + - - -
42D PHE* 4.3 4.5 - - + -
78D ALA* 4.0 2.2 - - + -
79D ARG 3.4 28.7 - - - +
80D ILE* 3.7 13.9 - - + -
88D THR* 1.3 72.1 - - - +
90D ASN* 1.3 60.6 + - - +
91D ILE* 3.8 17.5 - - + -
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Residues in contact with ASN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ASP* 3.2 24.4 - - - +
24D ARG* 3.6 32.3 + - - +
77D THR 3.5 3.3 - - - +
78D ALA* 3.2 5.7 - - - +
79D ARG* 2.7 42.8 + - + +
80D ILE 4.9 0.6 - - - -
81D ASP* 3.0 44.1 + - - +
82D PRO* 5.2 0.8 - - - +
84D ARG* 4.9 0.2 + - - -
88D THR* 3.8 2.1 - - - +
89D LEU* 1.3 72.8 - - - +
91D ILE* 1.3 59.8 + - - +
92D ASN* 5.6 0.4 - - - +
244D LEU* 5.0 8.8 - - + +
247D TYR* 4.1 5.1 - - - -
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Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.8 6.3 - - + -
21D VAL* 3.8 14.1 - - + -
22D ASP 3.0 9.0 + - - +
24D ARG* 2.9 26.6 + - - +
42D PHE* 3.5 34.8 - - + -
47D PHE* 5.7 1.1 - - + -
73D PRO* 4.3 5.6 - - + -
74D ASP 3.7 21.8 - - - +
75D PRO* 4.9 2.0 - - + -
77D THR* 3.8 4.0 - - - +
78D ALA* 3.9 15.3 - - + +
89D LEU* 3.8 18.2 - - + -
90D ASN* 1.3 81.0 - - - +
92D ASN* 1.3 76.7 + - - +
93D PHE* 3.3 20.2 - - + -
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Residues in contact with ASN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ARG* 3.3 24.6 - - - +
32D MET* 3.8 16.1 - - - +
74D ASP* 2.9 28.4 + - - +
77D THR* 2.8 28.8 + - + +
90D ASN* 5.6 0.9 - - - +
91D ILE* 1.3 75.0 - - - +
93D PHE* 1.3 63.7 + - - +
109D ARG* 4.0 13.4 - - - +
240D ASP* 3.0 34.4 + - - +
243D GLN* 5.6 1.2 - - - +
244D LEU* 6.3 0.4 - - - +
377D TYR* 3.8 7.3 + - - -
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Residues in contact with PHE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 5.6 0.9 - - + -
23D VAL* 3.7 35.2 - - + -
24D ARG 2.7 14.2 + - - +
25D PHE* 3.9 11.6 - - - +
37D ILE* 6.3 0.2 - - + -
42D PHE* 5.5 2.0 - + - -
46D VAL* 4.1 18.2 - - + -
51D LEU* 4.1 11.2 - - + -
71D LEU* 3.6 34.3 - - + -
72D LEU 3.3 8.7 - - - +
73D PRO* 3.3 37.7 - - + -
74D ASP 4.4 0.2 - - - +
91D ILE* 3.3 37.9 - - + -
92D ASN* 1.3 80.8 - - - +
94D PHE* 1.3 60.2 + - - +
95D VAL 4.1 0.5 + - - -
107D ASP* 4.4 1.7 - - - +
109D ARG* 3.3 23.4 + - - +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 3.3 4.7 - - - -
72D LEU* 2.8 37.7 + - + +
73D PRO 4.7 3.6 - - - -
74D ASP* 3.3 34.8 - - + -
93D PHE* 1.3 73.9 - - - +
95D VAL* 1.3 61.5 + - - +
96D HIS* 3.3 24.5 - - - +
107D ASP* 3.3 12.6 - - - +
109D ARG* 3.4 46.4 - - + -
113D ARG* 3.3 46.9 - - + +
236D LEU* 4.4 11.7 - - + -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 4.2 10.5 - - + -
26D CYS 5.1 0.4 - - - +
53D PHE* 3.9 15.9 - - + -
61D PHE* 3.9 21.3 - - + -
69D MET* 3.7 15.0 - - + -
70D LEU 3.4 9.0 - - - +
71D LEU* 3.8 17.5 - - + -
94D PHE* 1.3 73.3 - - - +
96D HIS* 1.3 66.3 + - - +
103D PRO* 3.8 1.6 - - - +
104D TYR* 2.9 42.5 + - + +
107D ASP* 2.7 36.4 + - + +
113D ARG* 5.3 0.2 + - - -
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Residues in contact with HIS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D MET* 3.4 11.3 - - - +
70D LEU* 2.7 50.0 + - + +
72D LEU* 3.5 31.0 - - + +
94D PHE* 3.3 41.3 - - + +
95D VAL* 1.3 76.9 - - - +
97D ASP* 1.3 65.7 + - - +
101D LEU 2.8 26.3 + - - +
102D GLU 3.3 10.1 + - - +
103D PRO* 3.9 21.3 - - + -
104D TYR 4.1 0.7 - - - +
113D ARG* 3.9 9.9 + - - -
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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