Contacts of the helix formed by residues 90 - 102 (chain F) in PDB entry 2XQL
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 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E GLY* 5.0 6.3 - - - +
47E ALA* 4.3 2.5 - - - -
86F ARG* 4.9 8.7 + - - -
88F THR* 3.4 16.9 + - - +
89F ILE* 1.3 77.5 - - - +
91F SER* 1.3 76.5 + - - +
92F ARG* 3.0 19.5 - - + +
93F GLU* 2.8 35.1 + - - +
94F ILE* 3.5 8.7 + - - +
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Residues in contact with SER 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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44E GLY* 6.0 0.2 - - - -
46E GLY* 3.8 29.3 - - - +
47E ALA* 4.1 4.8 - - - +
50E TYR* 4.1 20.1 - - - -
90F THR* 1.3 80.7 - - - +
92F ARG* 1.3 63.5 + - - +
93F GLU 3.0 2.7 - - - -
94F ILE* 3.1 13.0 + - - +
95F GLN* 3.0 24.3 + - - +
118F VAL* 4.7 9.3 - - - +
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Residues in contact with ARG 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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90F THR* 3.0 16.2 - - + +
91F SER* 1.3 85.1 + - - +
93F GLU* 1.3 67.1 + - - +
95F GLN* 3.9 14.8 - - - +
96F THR* 3.2 31.4 + - - +
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Residues in contact with GLU 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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77F ALA* 3.9 30.4 - - + +
80F LEU* 3.6 22.6 - - + +
81F ALA* 4.3 13.6 - - + +
84F ASN* 5.7 3.5 - - - +
86F ARG* 5.2 10.0 + - - +
88F THR 4.6 5.4 - - - -
89F ILE* 4.3 3.6 - - + -
90F THR* 2.8 52.5 + - - +
91F SER 3.0 0.6 - - - -
92F ARG* 1.3 85.4 + - - +
94F ILE* 1.3 59.3 + - - +
95F GLN 3.1 1.8 - - - -
96F THR* 4.7 0.2 - - - -
97F ALA* 2.8 31.5 + - - +
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Residues in contact with ILE 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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34E LEU* 5.1 5.4 - - + -
47E ALA* 4.0 18.8 - - + +
50E TYR* 3.6 23.1 - - + -
51E LEU* 3.9 39.7 - - + +
73F ILE* 4.1 9.0 - - + +
74F ALA* 5.6 0.4 - - - -
77F ALA* 4.0 11.0 - - + -
89F ILE* 3.9 21.8 - - + -
90F THR 3.6 11.7 - - - +
91F SER* 3.1 13.2 + - - +
93F GLU* 1.3 77.6 - - - +
95F GLN* 1.3 57.1 + - - +
97F ALA* 3.5 5.5 - - - +
98F VAL* 2.9 36.7 + - + +
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Residues in contact with GLN 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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50E TYR* 2.6 39.0 + - + +
91F SER 3.0 16.0 + - - +
92F ARG* 3.9 15.0 + - - +
94F ILE* 1.3 76.2 - - - +
96F THR* 1.3 61.7 + - - +
98F VAL* 3.0 6.0 + - - +
99F ARG* 2.9 50.1 + - - +
111F VAL* 3.2 23.4 - - + +
115F THR* 3.3 13.9 + - - +
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Residues in contact with THR 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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80F LEU* 3.5 31.0 - - + -
92F ARG* 3.2 27.3 + - - +
93F GLU* 4.7 0.2 - - - -
95F GLN* 1.3 74.9 + - - +
97F ALA* 1.3 67.0 + - - +
99F ARG* 3.1 15.1 + - + +
100F LEU* 3.0 34.3 + - + +
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Residues in contact with ALA 97 (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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73F ILE* 3.6 29.6 - - + +
76F GLU* 3.9 10.1 - - + -
77F ALA* 3.7 13.7 - - - +
80F LEU* 3.7 6.1 - - + +
93F GLU 2.8 19.9 + - - +
94F ILE* 3.5 5.6 - - - +
96F THR* 1.3 76.8 - - - +
98F VAL* 1.3 56.8 + - - +
100F LEU* 3.2 4.8 + - - +
101F LEU* 2.9 35.9 + - - +
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Residues in contact with VAL 98 (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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50E TYR* 4.6 2.5 - - + -
54E VAL* 3.9 22.2 - - + -
73F ILE* 3.9 27.4 - - + -
94F ILE* 2.9 23.3 + - + +
95F GLN* 3.0 9.4 + - - +
97F ALA* 1.3 74.9 - - - +
99F ARG* 1.3 65.4 + - - +
101F LEU* 4.6 0.4 - - - +
102F LEU* 3.0 34.1 + - + +
107F ALA* 4.0 11.2 - - - +
110F ALA* 3.8 26.2 - - + -
111F VAL* 4.1 11.7 - - + +
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Residues in contact with ARG 99 (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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95F GLN* 2.9 44.8 + - - +
96F THR* 3.1 15.7 + - + +
98F VAL* 1.3 78.9 - - - +
100F LEU* 1.3 65.2 + - + +
102F LEU 3.5 13.2 - - - +
107F ALA* 4.6 8.8 - - + +
108F LYS* 6.0 2.8 - - - +
111F VAL* 3.7 27.5 - - + +
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Residues in contact with LEU 100 (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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76F GLU* 3.9 24.9 - - + +
80F LEU* 4.4 9.6 - - + -
96F THR* 3.0 38.0 + - + +
97F ALA* 3.2 4.9 + - - +
99F ARG* 1.3 82.4 - - + +
101F LEU* 1.3 64.5 + - + +
102F LEU 4.6 1.0 - - - +
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Residues in contact with LEU 101 (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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96E LEU* 3.8 10.2 - - + +
72F ARG* 3.3 53.6 + - + +
73F ILE* 3.5 18.2 - - + +
76F GLU* 3.7 25.8 - - + +
97F ALA 2.9 19.2 + - - +
98F VAL* 5.1 0.2 - - - -
100F LEU* 1.3 78.6 - - + +
102F LEU* 1.3 73.7 + - + +
103F PRO* 3.4 8.8 - - - +
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Residues in contact with LEU 102 (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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54E VAL* 4.4 2.9 - - + -
58E LEU* 3.9 31.9 - - + -
96E LEU* 3.9 22.4 - - + -
69F ILE* 5.1 2.7 - - + -
73F ILE* 4.8 14.8 - - + -
98F VAL* 3.0 23.3 + - + +
99F ARG 3.5 14.2 - - - +
100F LEU 4.6 0.9 - - - +
101F LEU* 1.3 87.4 - - + +
103F PRO* 1.4 71.1 - - + +
106F LEU* 3.9 11.9 - - + +
107F ALA* 3.6 13.7 - - + +
110F ALA* 3.8 29.2 - - + -
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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