Contacts of the strand formed by residues 86 - 96 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D THR* 3.4 28.2 - - + +
57D THR 3.1 12.3 - - - +
58D ASP* 2.5 30.9 + - - +
59D ILE* 4.1 5.5 - - - +
84D PHE* 4.2 11.4 - - - +
85D PRO* 1.3 92.0 - - + +
87D ALA* 1.3 59.7 + - - +
88D ASN* 4.1 11.4 - - - +
108D THR* 4.4 4.9 - - - +
109D LEU* 5.2 0.2 - - - -
110D HIS 5.1 5.2 + - - -
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Residues in contact with ALA 87 (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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56D THR* 3.4 3.3 - - - +
57D THR* 2.9 34.2 + - - +
59D ILE* 4.1 8.6 - - + +
86D GLN* 1.3 74.0 - - - +
88D ASN* 1.3 62.5 + - - +
107D LEU* 4.6 1.1 - - + -
108D THR 3.2 14.6 - - - +
109D LEU* 4.2 7.0 - - + -
201D OTP 3.9 43.2 - - + +
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Residues in contact with ASN 88 (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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54D ASP* 5.7 0.9 - - - +
55D VAL 3.4 5.6 - - - +
56D THR* 3.0 40.8 + - - +
86D GLN* 4.1 9.7 - - - +
87D ALA* 1.3 76.0 + - - +
89D TYR* 1.3 60.0 + - - +
90D LYS* 4.9 16.4 - - + +
106D ASN 3.7 1.1 - - - +
107D LEU* 3.5 6.5 - - - +
108D THR* 2.8 53.3 + - - +
201D OTP 4.5 0.7 - - - -
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Residues in contact with TYR 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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53D VAL* 4.4 8.7 - - + -
54D ASP* 3.5 1.9 - - - -
55D VAL* 2.8 57.3 + - + +
88D ASN* 1.3 73.4 - - - +
90D LYS* 1.3 69.0 + - - +
91D GLY 4.3 0.4 - - - -
103D VAL* 3.1 38.8 + - + +
105D GLY* 3.3 12.3 + - - -
106D ASN 3.5 24.2 - - - -
107D LEU* 4.0 6.7 - - + -
116D LEU* 2.9 49.3 + - + -
118D LEU* 3.6 24.9 - - + +
201D OTP 3.7 18.1 - - + +
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Residues in contact with LYS 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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53D VAL 3.3 6.5 - - - +
54D ASP* 3.5 35.6 + - + +
88D ASN* 4.4 15.2 - - + +
89D TYR* 1.3 83.7 - - - +
91D GLY* 1.3 60.8 + - - +
105D GLY* 3.1 1.6 - - - -
106D ASN* 2.9 36.7 + - + +
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Residues in contact with GLY 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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52D THR* 3.2 7.3 - - - -
53D VAL* 2.8 31.7 + - - +
89D TYR* 4.3 2.8 - - - -
90D LYS* 1.3 75.8 - - - +
92D THR* 1.3 63.6 + - - -
103D VAL* 3.8 12.3 - - - -
104D VAL 3.3 12.3 - - - -
105D GLY* 3.7 2.9 - - - -
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Residues in contact with THR 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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50D THR* 6.0 1.6 - - - -
51D GLY 3.4 12.8 + - - +
52D THR* 4.7 6.7 - - + +
91D GLY* 1.3 75.5 + - - -
93D ILE* 1.4 72.2 + - - +
94D LYS* 3.7 19.2 + - - +
103D VAL* 3.3 4.5 - - - -
104D VAL* 2.8 38.2 + - - +
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Residues in contact with ILE 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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42D VAL* 3.7 29.4 - - + -
43D THR 3.9 5.2 - - - +
44D LEU* 4.1 11.4 - - + -
49D LYS 4.4 1.9 - - - +
50D THR* 4.3 3.5 - - - -
51D GLY* 2.9 27.7 + - - +
52D THR 3.9 11.7 - - - +
53D VAL* 4.0 17.7 - - + -
92D THR* 1.4 81.7 - - - +
94D LYS* 1.3 64.0 + - - +
95D PHE* 3.8 18.9 - - + -
100D PRO* 3.7 30.5 - - + -
102D SER 3.4 7.9 - - - +
103D VAL* 4.4 7.9 - - + +
120D ILE* 4.8 2.9 - - + -
201D OTP 4.9 7.6 - - + -
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Residues in contact with LYS 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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49D LYS 5.5 0.7 - - - -
92D THR* 3.9 25.6 - - + +
93D ILE* 1.3 76.6 - - - +
95D PHE* 1.3 58.0 + - - +
100D PRO* 3.5 4.5 - - - +
101D VAL* 2.8 32.4 + - + -
102D SER* 2.9 21.8 + - - +
104D VAL* 3.7 44.1 - - + +
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Residues in contact with PHE 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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44D LEU* 3.8 22.4 - - + -
46D ARG* 3.8 29.2 - - + -
49D LYS* 3.5 53.3 + - + -
50D THR 3.6 8.3 - - - -
93D ILE* 3.8 20.0 - - + -
94D LYS* 1.3 81.4 - - - +
96D ASP* 1.3 61.4 + - - +
97D GLY 4.2 7.6 - - - +
98D ASP 3.3 28.3 - - - -
99D LYS 3.2 11.4 - - - -
100D PRO* 3.7 13.9 - - + -
101D VAL* 3.9 2.8 - - - +
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Residues in contact with ASP 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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145A SER* 5.4 2.2 - - - -
159A PHE 4.5 0.5 - - - +
160A LYS* 3.4 23.7 - - + +
161A MET* 2.7 34.4 + - - +
162A LYS* 2.9 35.0 + - - +
95D PHE* 1.3 73.7 - - - +
97D GLY* 1.3 64.6 + - - +
98D ASP 3.7 1.4 + - - -
99D LYS* 2.9 18.0 + - - +
101D VAL* 3.6 28.0 - - + +
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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