Contacts of the helix formed by residues 99 - 113 (chain D) in PDB entry 2FO1
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 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A TYR* 3.6 36.3 - - + -
298A GLU 5.4 1.1 - - - +
299A ARG* 3.7 37.9 - - + +
346A GLN* 5.1 9.9 - - + -
348A PHE* 3.8 19.3 - - + -
95D VAL* 3.1 26.0 - - + +
96D THR* 4.4 4.9 - - - +
98D HIS* 1.3 93.9 - - + +
100D PHE* 1.3 54.5 + - - +
102D ARG* 3.1 20.2 - - + +
103D TYR* 2.7 34.5 + - - +
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Residues in contact with PHE 100 (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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348A PHE* 3.6 24.9 - + + -
350A GLY 3.6 11.0 - - - -
351A CYS* 4.6 0.9 - - - -
352A GLY* 3.5 37.9 - - - -
96D THR 4.7 0.4 - - - +
97D ALA* 2.7 32.8 + - + +
99D LEU* 1.3 69.5 - - - +
101D ASN* 1.3 77.0 + - + +
102D ARG 2.9 4.3 - - - -
103D TYR* 2.7 24.4 + + - +
104D THR* 2.9 33.5 + - + -
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Residues in contact with ASN 101 (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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97D ALA 2.8 23.0 - - - +
98D HIS* 2.9 23.5 + - - +
100D PHE* 1.3 90.2 - - + +
102D ARG* 1.3 58.4 + - - +
104D THR* 4.0 8.2 - - - -
105D GLU* 3.2 31.3 + - - +
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Residues in contact with ARG 102 (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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289A TYR* 3.2 34.0 + - - -
298A GLU* 3.6 40.3 + - - +
299A ARG* 3.5 23.0 + - - +
300A GLN* 5.2 1.6 - - - +
301A GLN* 5.1 2.0 - - - +
98D HIS* 3.1 30.3 - - + +
99D LEU* 3.1 19.8 - - + +
101D ASN* 1.3 81.2 - - - +
103D TYR* 1.3 62.9 + - - +
105D GLU* 3.8 14.5 - - - +
106D ASP* 3.2 40.1 + - - +
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Residues in contact with TYR 103 (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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282A GLN* 3.8 17.9 + - - -
285A GLU* 4.1 15.6 + - - +
287A VAL* 3.3 32.8 - - + +
289A TYR* 3.4 13.2 - - - +
301A GLN* 4.0 20.2 - - - -
348A PHE* 4.1 11.4 - + + -
350A GLY* 4.2 15.2 - - - -
99D LEU 2.7 11.9 + - - +
100D PHE* 2.7 17.7 + + - +
102D ARG* 1.3 76.5 - - - +
104D THR* 1.3 61.7 + - - -
106D ASP* 2.9 6.3 + - - +
107D GLU* 2.6 71.9 + - + +
110D LYS* 5.8 0.9 - - - -
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Residues in contact with THR 104 (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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279A HIS* 6.2 2.2 - - + -
100D PHE* 2.9 39.5 + - + -
101D ASN* 4.3 6.7 - - - -
103D TYR* 1.3 78.3 - - - +
105D GLU* 1.3 52.1 + - - +
107D GLU* 3.0 9.4 - - + +
108D GLU* 2.3 43.7 + - - +
111D ARG* 4.6 15.5 - - - +
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Residues in contact with GLU 105 (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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101D ASN* 3.2 23.0 + - - +
102D ARG* 3.8 18.1 - - - +
104D THR* 1.3 80.6 - - - +
106D ASP* 1.3 63.3 + - + +
107D GLU 3.1 0.7 - - - -
108D GLU* 3.6 14.9 - - - +
109D ARG* 3.6 20.4 + - - -
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Residues in contact with ASP 106 (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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289A TYR* 5.1 1.7 + - - +
301A GLN* 6.1 1.3 - - - -
102D ARG* 3.2 38.6 + - - +
103D TYR* 2.9 6.0 + - - +
105D GLU* 1.3 80.4 - - + +
107D GLU* 1.3 58.7 + - - +
109D ARG* 4.2 18.8 - - - +
110D LYS* 4.9 7.8 - - - +
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Residues in contact with GLU 107 (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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282A GLN* 3.3 32.4 + - - +
285A GLU* 5.1 2.6 - - - +
103D TYR* 2.6 47.0 + - + +
104D THR* 2.8 13.4 + - - +
106D ASP* 1.3 79.8 - - - +
108D GLU* 1.3 60.4 - - - +
109D ARG 3.2 1.8 - - - -
110D LYS* 2.7 56.9 + - - +
111D ARG* 3.7 17.4 + - - +
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Residues in contact with GLU 108 (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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104D THR* 2.3 31.0 + - + +
105D GLU* 3.6 15.0 - - - +
107D GLU* 1.3 71.1 - - - +
109D ARG* 1.3 56.4 + - - +
111D ARG* 2.7 64.8 + - - +
112D VAL* 2.8 28.3 + - + +
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Residues in contact with ARG 109 (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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105D GLU 3.6 16.1 + - - -
106D ASP* 4.2 19.3 - - - +
108D GLU* 1.3 74.8 - - - +
110D LYS* 1.3 64.8 + - + +
111D ARG 2.8 6.0 + - - -
112D VAL* 3.0 35.4 + - + +
113D GLU* 3.0 34.3 + - - +
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Residues in contact with LYS 110 (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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301A GLN* 5.4 6.0 + - - -
303A ASP* 5.9 0.8 + - - -
305A SER* 5.6 7.9 - - - -
103D TYR* 5.8 1.4 - - - -
106D ASP 4.9 7.6 - - - +
107D GLU* 2.7 41.0 + - - +
108D GLU 3.3 0.4 - - - -
109D ARG* 1.3 77.9 - - + +
111D ARG* 1.3 55.9 + - + +
113D GLU* 3.9 9.1 - - - +
114D GLN* 2.7 37.2 - - - +
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A HIS* 3.8 26.6 + - - -
282A GLN* 3.3 33.9 + - - +
104D THR* 4.4 11.1 + - - +
107D GLU* 3.7 23.7 + - - +
108D GLU* 2.7 49.7 + - - +
110D LYS* 1.3 82.0 - - + +
112D VAL* 1.3 63.0 + - - +
113D GLU 3.3 0.6 + - - -
114D GLN* 4.0 19.2 + - - +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D GLU* 2.8 37.5 + - + +
109D ARG* 3.0 39.7 + - - +
111D ARG* 1.3 74.3 - - - +
113D GLU* 1.3 67.6 + - + +
114D GLN 3.3 6.1 + - - -
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Residues in contact with GLU 113 (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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109D ARG* 3.0 37.8 + - - +
110D LYS* 3.9 7.1 - - - +
112D VAL* 1.3 81.0 - - + +
114D GLN* 1.3 71.3 + - - +
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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