Contacts of the helix formed by residues 96 - 111 (chain F) in PDB entry 4O9U
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 96 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F ARG* 6.0 0.8 - - - +
75F GLN* 4.0 25.1 - - - +
76F PRO* 4.5 2.2 - - + -
94F PHE* 3.3 37.3 - - + +
95F VAL* 1.3 87.2 - - - +
97F PRO* 1.4 64.9 - - - +
98F HIS* 3.1 12.2 + - + +
99F LYS* 3.5 7.5 + - + +
100F ASN* 2.8 26.6 + - - +
118F GLU* 2.9 22.7 + - + +
132F LEU* 5.7 1.2 - - - +
287F GLU* 5.4 5.9 + - - -
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Residues in contact with PRO 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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95F VAL* 3.5 4.9 - - + -
96F GLN* 1.4 82.9 - - - +
98F HIS* 1.3 69.8 + - + +
99F LYS 3.3 1.1 - - - -
100F ASN 3.8 1.6 - - - -
101F LEU* 3.1 31.4 + - + +
104F VAL* 3.8 37.5 - - + -
118F GLU* 4.3 6.3 - - + +
357F LEU* 5.3 11.4 - - + -
368F THR* 5.8 10.5 - - + +
372F LEU* 5.6 5.8 - - + -
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Residues in contact with HIS 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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96F GLN* 3.1 4.4 + - + -
97F PRO* 1.3 89.0 - - + +
99F LYS* 1.3 63.2 + - + +
101F LEU* 5.0 0.7 - - - -
260F GLY* 3.1 40.8 + - - -
288F SER* 6.3 2.2 - - - -
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Residues in contact with LYS 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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75F GLN* 5.7 5.4 - - - +
96F GLN* 3.5 8.0 + - + +
98F HIS* 1.3 81.5 - - + +
100F ASN* 1.3 76.8 + - - +
101F LEU* 3.8 1.6 - - - -
103F LEU* 5.1 0.9 - - - +
287F GLU* 5.1 16.5 + - - +
312F LEU* 5.6 10.5 - - - +
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Residues in contact with ASN 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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75F GLN* 4.3 9.4 + - - +
76F PRO* 3.1 32.0 - - + +
95F VAL 3.2 7.8 + - - +
96F GLN* 2.8 32.2 + - - +
97F PRO 4.0 0.4 - - - -
99F LYS* 1.3 95.5 - - - +
101F LEU* 1.3 64.8 + - - +
102F GLU 3.1 3.1 - - - -
103F LEU* 2.8 44.2 + - + +
104F VAL* 2.8 17.0 + - + +
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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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97F PRO* 3.1 20.0 + - + +
98F HIS 5.8 0.2 - - - -
99F LYS 3.8 1.2 - - - -
100F ASN* 1.3 74.7 - - - +
102F GLU* 1.3 74.3 + - - +
104F VAL* 3.3 9.1 + - - +
105F ARG* 2.9 27.5 + - - +
371F LEU* 4.7 20.9 - - + -
372F LEU* 3.7 41.0 - - + +
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Residues in contact with GLU 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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79F GLU* 4.0 9.7 - - - +
100F ASN 3.1 1.0 - - - -
101F LEU* 1.3 96.1 - - - +
103F LEU* 1.3 62.8 + - + +
105F ARG* 3.5 30.6 + - - +
106F ALA* 3.2 22.9 + - - +
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Residues in contact with LEU 103 (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 PRO* 4.9 14.4 - - + +
77F PRO 4.3 11.6 - - - +
78F PRO* 4.5 7.4 - - + -
79F GLU* 3.1 42.2 - - + +
82F ILE* 3.4 8.1 - - - +
99F LYS 5.1 0.9 - - - +
100F ASN* 2.8 40.0 + - + +
102F GLU* 1.3 77.5 - - + +
104F VAL* 1.3 64.4 + - - +
106F ALA* 3.4 8.2 + - - +
107F LEU* 3.2 20.5 + - - +
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Residues in contact with VAL 104 (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 PRO* 5.8 0.7 - - + -
95F VAL* 3.7 32.3 - - + +
97F PRO* 3.8 32.5 - - + -
100F ASN* 2.8 18.7 + - + +
101F LEU* 3.4 9.2 - - - +
103F LEU* 1.3 74.6 - - - +
105F ARG* 1.3 63.4 + - - +
106F ALA 3.1 2.3 + - - -
107F LEU* 3.3 15.9 + - - +
108F GLN* 3.3 14.2 + - - +
357F LEU* 5.1 5.4 - - + -
358F MET* 4.0 12.7 - - + +
363F VAL* 5.6 5.8 - - + -
372F LEU* 4.3 20.0 - - + -
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Residues in contact with ARG 105 (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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79F GLU* 5.2 1.8 + - - -
101F LEU* 2.9 16.7 + - + +
102F GLU* 3.5 36.6 + - - +
104F VAL* 1.3 74.8 - - - +
106F ALA* 1.3 63.2 + - - +
107F LEU 3.4 0.2 - - - -
108F GLN* 3.3 28.9 - - + +
109F ALA* 3.2 40.2 + - - +
372F LEU* 3.5 15.7 - - + +
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Residues in contact with ALA 106 (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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79F GLU* 3.3 33.4 - - + +
82F ILE* 3.2 23.8 - - + +
83F GLN* 5.3 4.0 + - - +
102F GLU 3.2 11.4 + - - +
103F LEU 3.4 10.5 - - - +
104F VAL 3.1 0.4 - - - -
105F ARG* 1.3 87.6 - - - +
107F LEU* 1.3 61.4 + - - +
109F ALA* 3.8 2.4 + - - +
110F LYS* 3.6 14.0 + - - +
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Residues in contact with LEU 107 (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 PRO* 6.3 0.7 - - + -
77F PRO* 3.9 25.1 - - + -
82F ILE* 3.7 30.7 - - + -
85F LEU* 3.8 22.0 - - + -
91F VAL* 4.5 7.0 - - + -
95F VAL* 5.4 8.5 - - + -
103F LEU 3.2 8.4 + - - +
104F VAL* 3.3 10.3 + - - +
106F ALA* 1.3 79.9 - - - +
108F GLN* 1.3 60.1 + - - +
110F LYS* 3.7 1.7 + - - +
111F LYS 3.5 15.1 + - - -
112F ALA* 3.5 27.8 + - + +
114F VAL* 3.9 26.5 - - + -
358F MET* 3.6 14.4 - - + +
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Residues in contact with GLN 108 (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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104F VAL 3.3 6.1 + - - +
105F ARG* 3.3 41.2 - - + +
107F LEU* 1.3 76.5 - - - +
109F ALA* 1.3 63.1 + - + +
110F LYS 3.3 0.7 - - - -
111F LYS* 4.0 8.8 + - - +
358F MET* 3.8 15.2 - - + -
361F GLY* 3.6 22.9 + - - +
363F VAL* 3.5 21.4 - - + +
372F LEU* 3.4 23.3 - - - +
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Residues in contact with ALA 109 (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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105F ARG* 3.2 38.3 + - - +
106F ALA* 4.1 4.5 - - - +
107F LEU 3.4 0.2 - - - -
108F GLN* 1.3 79.8 - - + +
110F LYS* 1.3 60.5 + - - +
111F LYS* 3.5 5.4 - - - +
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Residues in contact with LYS 110 (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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82F ILE* 3.4 33.9 - - + +
83F GLN* 4.1 32.5 - - + +
85F LEU* 4.9 15.7 - - + -
86F GLU 6.4 0.4 - - - -
106F ALA 3.6 15.2 + - - +
107F LEU 3.7 4.0 + - - +
108F GLN 3.3 0.2 - - - -
109F ALA* 1.3 79.8 - - - +
111F LYS* 1.3 73.7 + - - +
112F ALA* 4.9 5.6 - - + +
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Residues in contact with LYS 111 (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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86F GLU 5.5 0.5 - - - +
87F PRO* 5.4 4.0 - - - +
88F GLY 5.2 6.4 + - - -
107F LEU 3.5 3.6 + - - -
108F GLN 4.0 7.9 + - - +
109F ALA 3.5 7.1 - - - +
110F LYS* 1.3 85.7 - - - +
112F ALA* 1.3 59.3 + - - +
360F GLU* 3.5 34.6 - - + +
361F GLY* 3.8 7.2 - - - -
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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