Contacts of the strand formed by residues 113 - 121 (chain X) in PDB entry 1T6B
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 LEU 113 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68X PHE* 4.0 27.3 - - + -
69X ILE 3.7 3.4 - - - +
70X LYS* 3.5 34.5 - - + +
92X ASP* 4.1 1.9 - - - +
111X GLY 4.2 8.5 - - - +
112X ARG* 1.3 99.3 + - - +
114X TYR* 1.3 61.9 + - - +
152X GLN* 4.1 24.0 - - - +
465X GLU* 4.6 18.2 - - + +
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Residues in contact with TYR 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X PHE* 3.2 7.2 - - - -
69X ILE* 3.1 46.8 + - + -
70X LYS* 5.5 0.2 - - - -
71X VAL* 5.4 2.5 - - + -
91X VAL* 4.4 7.6 - - + -
92X ASP* 3.4 25.6 - - + +
106X ILE* 6.2 0.2 - - + -
107X ARG 4.5 3.5 + - - -
108X LEU* 3.5 38.8 - - + -
109X GLU* 2.8 46.8 + - - +
112X ARG* 3.5 45.6 + - + +
113X LEU* 1.3 76.7 - - - +
115X GLN* 1.3 67.3 + - - +
116X ILE* 3.8 0.9 - - - +
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Residues in contact with GLN 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X GLY 3.6 6.7 - - - +
68X PHE* 3.4 29.5 - - + -
90X TRP 4.6 0.4 - - - -
91X VAL* 3.3 7.3 - - - +
92X ASP* 2.8 43.2 + - - +
93X ASP* 4.0 19.0 + - - +
114X TYR* 1.3 74.1 - - - +
116X ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X LEU* 4.1 26.9 - - + -
65X TRP 5.1 1.1 - - - +
66X SER* 3.6 4.7 + - - -
67X GLY 2.9 33.5 + - - +
68X PHE 4.0 1.3 - - - -
69X ILE* 3.5 49.6 - - + +
79X PHE* 5.2 1.6 - - + -
89X MET* 3.9 13.7 - - + -
90X TRP 3.6 1.8 - - - -
91X VAL* 3.7 24.5 - - + -
115X GLN* 1.3 78.6 - - - +
117X LYS* 1.3 72.9 + - - +
118X ILE* 4.4 11.7 - - + +
134X LEU* 5.6 0.9 - - + -
151X LEU* 5.2 4.3 - - + -
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Residues in contact with LYS 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X ILE* 4.5 16.2 - - + -
65X TRP 3.4 9.9 - - - +
66X SER* 3.1 26.5 + - - +
89X MET* 3.3 5.4 - - - +
90X TRP* 3.0 58.0 + - + +
116X ILE* 1.3 74.7 - - - +
118X ILE* 1.3 65.0 + - - +
119X GLN* 6.1 0.4 - - + -
175X VAL* 4.8 22.6 - - - +
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Residues in contact with ILE 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X LEU* 4.4 11.7 - - + -
43X LEU* 4.4 17.7 - - + -
64X ILE* 3.4 8.5 - - - +
65X TRP* 2.9 50.8 + - + +
81X THR* 4.8 2.2 - - + -
87X VAL* 3.8 25.6 - - + -
88X THR 3.5 2.5 - - - +
89X MET* 3.7 22.4 - - + -
116X ILE* 4.4 5.8 - - + -
117X LYS* 1.3 80.0 - - - +
119X GLN* 1.3 65.8 + - - +
132X PHE* 4.2 13.7 - - + -
134X LEU* 3.8 32.8 - - + -
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Residues in contact with GLN 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X PHE* 3.7 27.1 - - + -
63X ALA 3.7 4.0 - - - -
64X ILE* 4.7 4.9 - - + -
86X HIS 4.4 2.0 + - - -
87X VAL* 3.2 11.5 - - - +
88X THR* 2.8 59.1 + - - +
90X TRP* 3.8 21.7 - - + -
99X LYS* 5.0 5.5 - - - +
117X LYS* 6.1 0.4 - - + -
118X ILE* 1.3 76.4 - - - +
120X TYR* 1.3 63.8 + - - +
121X GLN* 3.7 20.4 + - - +
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Residues in contact with TYR 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X PHE* 4.1 0.3 - - - -
60X PHE* 4.5 9.8 + - + -
61X GLN 4.4 3.8 - - - -
62X SER* 2.9 31.0 - - - -
63X ALA 2.9 26.8 + - - +
65X TRP* 4.0 15.3 - + + -
83X ALA* 4.0 21.8 - - + -
86X HIS* 3.3 17.3 - - + -
87X VAL* 4.0 10.5 - - + -
119X GLN* 1.3 76.8 - - - +
121X GLN* 1.3 62.1 + - - +
122X ARG* 2.8 49.9 + - + +
130X LEU* 3.4 35.0 - - + +
131X ASP 6.1 0.2 - - - -
132X PHE* 3.8 24.5 - + + -
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Residues in contact with GLN 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X LEU* 3.3 37.6 + - + +
28X ASN* 4.7 4.6 - - - +
29X PHE* 3.9 25.8 - - + -
61X GLN 3.5 3.4 - - - -
86X HIS* 3.0 36.2 + - - +
99X LYS* 5.7 3.7 + - - +
119X GLN* 3.7 18.9 + - - +
120X TYR* 1.3 79.5 - - - +
122X ARG* 1.3 60.0 + - - +
123X GLU 4.2 0.4 + - - -
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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