Contacts of the strand formed by residues 86 - 96 (chain C) in PDB entry 5IXG
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 GLN 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C THR* 3.5 26.8 - - + +
57C THR 3.2 8.7 - - - +
58C ASP* 2.9 28.1 + - - +
59C ILE* 4.1 6.6 - - - +
84C PHE* 3.2 10.4 - - - +
85C PRO* 1.3 94.2 - - + +
87C ALA* 1.3 60.0 + - - +
108C THR* 4.5 4.0 - - - +
109C LEU* 5.1 0.2 - - - -
110C HIS 5.0 6.1 + - - -
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Residues in contact with ALA 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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56C THR* 3.3 6.1 - - - +
57C THR* 2.9 32.7 + - - +
59C ILE* 4.2 3.6 - - + +
86C GLN* 1.3 75.0 - - - +
88C ASN* 1.3 60.2 + - - +
107C LEU* 4.7 1.1 - - + -
108C THR 3.2 14.6 - - - +
109C LEU* 4.0 12.6 - - + +
201C OTP 3.9 39.7 - - + +
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Residues in contact with ASN 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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54C ASP* 3.1 21.4 + - - -
55C VAL 2.8 22.7 + - - -
56C THR* 3.3 14.9 + - + +
86C GLN* 6.3 0.2 - - + -
87C ALA* 1.3 74.2 - - - +
89C TYR* 1.3 58.1 + - - +
90C LYS* 2.8 36.9 + - - +
106C ASN 3.8 1.2 - - - +
107C LEU* 3.4 7.6 - - - +
108C THR* 2.8 49.5 + - + +
201C OTP 4.4 1.1 - - - -
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Residues in contact with TYR 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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53C VAL* 3.9 8.9 - - + +
54C ASP* 3.5 2.8 - - - -
55C VAL* 2.9 53.8 + - + +
88C ASN* 1.3 72.4 - - - +
90C LYS* 1.3 68.5 + - - +
91C GLY 4.2 0.2 - - - -
103C VAL* 3.1 41.7 + - + +
105C GLY* 3.4 10.8 + - - -
106C ASN 3.4 23.6 - - - -
107C LEU* 4.2 4.9 - - + -
116C LEU* 2.9 50.0 + - + -
118C LEU* 3.9 21.9 - - + +
201C OTP 3.7 19.2 - - + +
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Residues in contact with LYS 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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53C VAL 3.3 7.4 - - - +
54C ASP* 3.8 25.8 + - + +
88C ASN* 2.8 39.6 + - - +
89C TYR* 1.3 82.0 - - - +
91C GLY* 1.3 58.2 + - - +
105C GLY* 3.2 1.4 - - - -
106C ASN* 2.9 36.6 + - + +
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Residues in contact with GLY 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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52C THR* 3.2 8.5 + - - -
53C VAL 2.8 32.3 + - - +
89C TYR* 4.2 2.0 - - - -
90C LYS* 1.3 75.6 - - - +
92C THR* 1.3 64.0 + - - -
103C VAL* 3.8 13.5 - - - -
104C VAL 3.3 11.9 - - - -
105C GLY* 3.7 3.8 - - - -
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Residues in contact with THR 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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50C THR* 3.6 16.2 - - - +
51C GLY 3.3 12.3 + - - +
52C THR* 5.4 2.3 + - - -
91C GLY* 1.3 75.3 - - - -
93C ILE* 1.3 64.7 + - - +
94C LYS* 3.4 29.8 - - + +
103C VAL* 3.4 3.3 - - - -
104C VAL 2.8 32.8 + - - -
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Residues in contact with ILE 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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42C VAL* 3.7 19.7 - - + -
44C LEU* 3.3 30.5 - - + -
49C LYS 4.2 0.7 - - - +
50C THR* 3.6 24.8 + - - -
51C GLY* 2.8 25.7 + - - +
53C VAL* 4.1 19.5 - - + -
92C THR* 1.3 74.0 - - - +
94C LYS* 1.3 63.3 - - - +
95C PHE* 3.8 19.4 - - + -
100C PRO* 3.9 22.9 - - + -
102C SER 3.5 9.6 - - - +
103C VAL* 4.2 9.6 - - + +
120C ILE* 4.6 3.1 - - + -
201C OTP 4.8 7.2 - - + -
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Residues in contact with LYS 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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49C LYS 5.2 0.7 - - - -
92C THR* 3.4 41.4 - - + +
93C ILE* 1.3 74.6 - - - +
95C PHE* 1.3 64.3 + - - +
100C PRO* 3.6 2.9 - - - +
101C VAL* 2.8 28.8 + - + +
102C SER* 2.9 30.3 + - - +
104C VAL* 3.7 30.6 - - + +
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Residues in contact with PHE 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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44C LEU* 5.0 5.8 - - + -
46C ARG* 3.9 30.7 - - + -
49C LYS* 3.2 38.4 + - + -
50C THR* 3.2 35.4 - - - -
93C ILE* 3.8 13.7 - - + -
94C LYS* 1.3 81.1 - - - +
96C ASP* 1.3 57.2 + - - +
97C GLY 3.6 12.6 + - - +
98C ASP 3.7 13.5 - - - -
99C LYS 3.2 8.3 - - - +
100C PRO* 3.5 36.1 - - + -
101C VAL* 3.8 5.0 - - - +
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Residues in contact with ASP 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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145B SER* 5.3 2.7 - - - -
159B PHE 4.7 0.9 - - - +
160B LYS* 3.2 38.3 - - + +
161B MET* 2.8 35.0 + - - +
162B LYS* 3.0 35.5 + - - +
95C PHE* 1.3 69.5 - - - +
97C GLY* 1.3 60.8 + - - +
99C LYS* 2.8 14.2 + - - +
101C VAL* 2.9 30.8 - - + +
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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