Contacts of the strand formed by residues 88 - 96 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ASP* 4.4 0.9 + - - -
18F VAL* 4.4 4.0 - - - -
20F TYR* 3.2 19.6 - - + +
22F ASP* 3.9 11.9 - - + +
80F ILE* 3.5 6.1 - - - +
81F ASP* 2.8 39.7 + - - +
84F ARG* 3.2 47.3 + - - +
86F ALA 2.7 20.5 + - - -
87F LYS* 1.3 75.6 + - - +
89F LEU* 1.3 58.6 + - - +
90F ASN* 3.9 13.2 - - - +
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.8 29.8 - - + +
12F LEU* 3.8 19.5 - - + -
13F ALA* 4.2 20.9 - - + +
18F VAL* 3.9 19.3 - - + +
20F TYR 3.0 7.0 + - - +
21F VAL* 3.3 10.8 - - + +
22F ASP 2.9 23.2 + - - -
42F PHE* 4.3 4.7 - - + -
78F ALA* 4.0 2.5 - - + -
79F ARG 3.4 29.6 - - - +
80F ILE* 3.8 13.2 - - + -
88F THR* 1.3 71.4 - - - +
90F ASN* 1.3 64.5 + - - +
91F ILE* 3.9 12.3 - - + -
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Residues in contact with ASN 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ASP* 3.3 22.6 - - - +
24F ARG* 3.6 32.9 + - - +
77F THR 3.6 3.0 - - - +
78F ALA* 3.2 5.4 - - - +
79F ARG* 2.8 42.8 + - + +
80F ILE 4.9 0.6 + - - -
81F ASP* 3.1 44.5 + - - +
82F PRO* 5.1 0.4 - - - +
84F ARG* 4.9 0.2 + - - -
88F THR* 3.9 2.3 - - - +
89F LEU* 1.3 73.5 - - - +
91F ILE* 1.3 61.0 + - - +
92F ASN* 5.7 0.7 - - - +
244F LEU* 5.0 8.5 - - + +
247F TYR* 4.1 5.5 - - - -
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Residues in contact with ILE 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.8 12.6 - - + -
21F VAL* 3.8 16.2 - - + -
22F ASP 3.0 7.9 + - - +
24F ARG* 2.8 26.6 + - - +
42F PHE* 3.4 39.0 - - + -
47F PHE* 5.6 1.1 - - + -
73F PRO* 4.3 5.2 - - + -
74F ASP 3.7 21.1 - - - +
75F PRO* 4.9 2.7 - - + -
77F THR* 3.8 4.0 - - - +
78F ALA* 4.1 13.9 - - + +
89F LEU* 3.9 8.5 - - + -
90F ASN* 1.3 80.5 - - - +
92F ASN* 1.3 77.1 + - - +
93F PHE* 3.4 19.1 - - + -
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Residues in contact with ASN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ARG* 3.3 25.1 - - - +
32F MET* 3.8 16.4 - - - +
74F ASP* 2.9 24.8 + - - +
77F THR* 2.8 33.2 + - + +
90F ASN* 5.7 0.7 - - - +
91F ILE* 1.3 74.1 - - - +
93F PHE* 1.3 63.4 + - - +
109F ARG* 3.9 14.3 - - - +
240F ASP* 3.0 35.4 + - - +
243F GLN* 5.6 0.8 - - - +
244F LEU* 6.4 0.2 - - - +
377F TYR* 3.8 6.7 + - - -
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Residues in contact with PHE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F VAL* 5.6 0.7 - - + -
23F VAL* 3.6 40.6 - - + -
24F ARG 2.6 14.3 + - - +
25F PHE* 3.9 11.9 - - - +
42F PHE* 5.4 1.3 - + - -
46F VAL* 4.0 19.5 - - + -
51F LEU* 4.2 6.7 - - + -
71F LEU* 3.6 29.2 - - + -
72F LEU 3.3 14.1 - - - +
73F PRO* 3.3 40.2 - - + -
74F ASP 4.3 0.2 - - - +
91F ILE* 3.4 37.7 - - + -
92F ASN* 1.3 78.8 - - - +
94F PHE* 1.3 59.9 + - - +
95F VAL 4.2 0.3 + - - -
107F ASP* 4.5 1.4 - - - +
109F ARG* 3.3 24.2 + - - -
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Residues in contact with PHE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LEU* 3.2 6.4 - - - -
72F LEU* 2.8 41.2 + - + +
73F PRO 4.7 3.8 - - - -
74F ASP* 3.4 34.1 - - + -
93F PHE* 1.3 72.2 - - - +
95F VAL* 1.3 62.9 + - - +
96F HIS* 3.5 20.7 - - + +
107F ASP* 3.3 10.5 - - - +
109F ARG* 3.5 46.7 - - + -
113F ARG* 3.3 45.5 - - + +
236F LEU* 4.4 11.4 - - + -
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Residues in contact with VAL 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F PHE* 4.1 12.8 - - + -
26F CYS 5.2 0.4 - - - +
53F PHE* 3.9 17.0 - - + -
61F PHE* 4.0 20.2 - - + -
69F MET* 3.8 14.1 - - + -
70F LEU 3.3 10.1 - - - +
71F LEU* 3.8 16.2 - - + -
94F PHE* 1.3 73.1 - - - +
96F HIS* 1.3 66.1 + - - +
103F PRO* 3.8 1.9 - - - +
104F TYR* 2.9 42.3 + - + +
107F ASP* 2.8 33.7 + - + +
110F ASN* 5.5 0.2 - - - +
113F ARG* 5.3 0.5 + - - -
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Residues in contact with HIS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F MET* 3.5 10.4 - - - +
70F LEU* 2.7 49.3 + - + +
72F LEU* 3.6 31.3 - - + +
94F PHE* 3.5 31.2 - - + +
95F VAL* 1.3 80.6 - - - +
97F ASP* 1.3 65.8 + - - +
101F LEU 2.8 25.6 + - - +
102F GLU 3.3 9.9 - - - +
103F PRO* 3.9 21.5 - - + -
104F TYR 4.1 1.1 - - - +
113F ARG* 3.9 9.2 + - - -
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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