Contacts of the strand formed by residues 92 - 100 (chain C) in PDB entry 5TZ2
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 GLY 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B NAG 4.0 19.7 - - - -
42C PHE* 3.9 7.2 - - - -
90C HIS 3.9 1.8 + - - -
91C THR* 1.3 75.2 - - - +
93C ASN* 1.3 64.5 + - - -
94C TYR* 3.7 4.2 + - - -
110C GLU* 3.4 4.8 - - - -
111C LEU* 2.7 41.3 + - - +
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Residues in contact with ASN 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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1B NAG 1.4 61.6 + - - +
41C LYS 4.1 2.8 - - - +
42C PHE* 3.6 17.2 - - - -
43C LYS* 4.3 5.3 + - - +
92C GLY* 1.3 70.5 - - - -
94C TYR* 1.3 63.6 + - - +
95C THR* 4.1 2.5 + - - +
108C ILE* 3.8 22.2 - - + +
109C ILE 3.6 0.7 - - - -
110C GLU* 3.2 22.2 + - - +
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 3.5 28.3 - - + -
40C TRP* 3.7 21.8 - + + -
41C LYS 3.4 6.3 - - - -
42C PHE* 3.6 33.0 - + + -
47C ILE* 4.2 12.8 - - + -
63C PHE* 3.7 19.4 - + - -
80C LEU* 4.6 0.2 - - + -
82C MET* 4.2 5.8 - - + +
90C HIS* 2.6 43.0 + - - +
92C GLY 3.7 9.4 - - - -
93C ASN* 1.3 73.0 - - - +
95C THR* 1.3 62.2 + - - +
107C THR 3.9 0.5 - - - +
108C ILE* 3.3 4.7 - - - +
109C ILE* 2.6 42.7 + - - +
111C LEU* 3.7 25.1 - - + +
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Residues in contact with THR 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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39C LYS 3.6 2.1 - - - +
40C TRP* 3.4 7.8 - - - -
41C LYS* 2.8 61.1 + - + +
93C ASN* 4.1 2.8 + - - +
94C TYR* 1.3 74.1 + - - +
96C CYS* 1.3 62.1 + - - +
97C GLU* 4.4 1.3 - - + +
106C GLU* 3.7 37.0 - - + +
107C THR 3.6 7.6 - - - +
108C ILE* 3.9 17.2 - - + +
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Residues in contact with CYS 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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4C PHE* 4.6 0.5 - - - -
23C CYS* 2.0 49.1 - - + -
38C VAL* 4.9 2.0 - - - -
39C LYS 4.1 2.2 - - - -
40C TRP* 3.6 35.2 - - + -
78C ALA* 4.2 3.8 - - - -
94C TYR 4.0 1.2 + - - -
95C THR* 1.3 69.2 - - - +
97C GLU* 1.3 59.3 + - - +
98C VAL* 3.7 14.9 + - - +
106C GLU* 3.2 5.9 - - - -
107C THR* 2.8 36.1 + - + +
109C ILE* 4.1 0.4 - - + -
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Residues in contact with GLU 97 (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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37C TYR* 3.9 1.3 - - - +
38C VAL* 3.6 3.3 - - - +
39C LYS* 2.9 70.1 + - + +
41C LYS* 3.2 25.6 - - - -
95C THR* 3.6 3.2 + - + -
96C CYS* 1.3 72.0 - - - +
98C VAL* 1.3 64.0 + - - +
99C THR* 4.1 9.9 + - - +
104C GLU* 3.4 29.0 - - + +
105C GLY 3.6 4.9 - - - +
106C GLU* 3.8 18.4 - - + +
102H PHE* 5.6 3.5 - - - -
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Residues in contact with VAL 98 (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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2C LEU* 3.4 14.8 - - + +
4C PHE* 4.4 3.1 - - + -
23C CYS* 4.2 3.4 - - - -
25C VAL* 4.2 30.1 - - + -
28C MET* 5.0 5.4 - - - -
36C VAL* 4.5 8.1 - - + -
37C TYR 3.8 1.6 - - - -
38C VAL* 4.5 15.3 - - + +
73C LEU* 6.2 0.2 - - + -
78C ALA* 4.4 11.4 - - + -
96C CYS* 3.8 25.6 - - - +
97C GLU* 1.3 76.2 - - - +
99C THR* 1.3 69.1 + - - +
100C GLU* 4.6 5.2 - - + -
104C GLU* 3.5 1.4 - - - -
105C GLY 2.9 35.7 + - - +
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Residues in contact with THR 99 (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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35C GLU 3.7 0.9 - - - +
36C VAL* 3.3 6.1 - - - +
37C TYR* 2.7 56.2 + - - +
97C GLU* 4.1 10.7 + - - +
98C VAL* 1.3 71.9 - - - +
100C GLU* 1.3 60.5 + - - +
101C LEU 4.7 0.2 - - - +
103C ARG 3.9 4.7 - - - +
104C GLU* 3.4 18.1 - - + +
103H ALA* 4.0 10.6 - - + +
32L ARG* 3.8 15.5 - - - +
50L TRP* 3.7 31.6 - - + -
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Residues in contact with GLU 100 (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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2C LEU* 3.9 17.2 - - + +
28C MET* 4.0 22.2 - - + -
29C GLU* 3.1 17.1 + - - +
30C ALA* 2.7 45.9 + - + +
35C GLU 3.7 2.9 - - - -
36C VAL* 4.6 3.6 - - + +
98C VAL* 3.8 6.6 + - + -
99C THR* 1.3 72.5 - - - +
101C LEU* 1.3 64.9 + - - +
102C THR 3.0 0.7 + - - -
103C ARG* 2.9 62.5 + - - +
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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