Contacts of the helix formed by residues 96 - 108 (chain F) in PDB entry 7KHI
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 ASP 96 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F THR 4.2 0.7 - - - +
95F THR* 1.3 80.7 + - - +
97F PRO* 1.3 75.0 - - - +
98F VAL* 2.9 40.6 + - - +
99F ARG* 3.2 26.8 + - + +
100F MET* 3.4 7.8 + - - +
55X G 3.3 22.0 + - - +
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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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294D ASN* 5.2 1.3 - - - +
297D ARG* 4.5 20.4 - - + +
298D MET* 6.4 0.9 - - - -
301D GLU* 4.6 30.3 - - + +
95F THR 3.0 7.4 - - - +
96F ASP* 1.3 89.1 - - - +
98F VAL* 1.3 62.8 + - + +
99F ARG 3.3 0.2 - - - -
100F MET* 3.1 17.9 - - + +
101F TYR* 3.0 27.0 + - - +
402F LEU* 3.9 24.0 - - + -
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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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96F ASP* 2.9 26.1 + - - +
97F PRO* 1.3 77.6 - - - +
99F ARG* 1.3 57.1 + - - +
101F TYR* 3.4 4.3 + - - +
102F MET* 2.8 41.9 + - + +
401F PHE* 5.2 15.0 - - + -
402F LEU* 3.8 26.5 - - + -
55X G 3.6 44.2 - - + +
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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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37F ASP* 4.3 25.0 - - - +
38F SER* 5.3 2.2 - - - +
94F THR* 4.2 29.0 - - + +
96F ASP* 3.2 22.5 + - + +
98F VAL* 1.3 76.2 - - - +
100F MET* 1.3 64.3 + - - +
102F MET* 3.1 9.7 + - - +
103F ARG* 3.0 29.6 + - - +
55X G 3.1 44.7 + - - +
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Residues in contact with MET 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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140D TYR* 4.3 15.0 - - + -
142D GLU* 3.8 23.8 - - + +
297D ARG* 3.3 36.1 - - - +
94F THR* 2.9 35.8 + - - +
95F THR* 2.9 23.1 - - - +
96F ASP 3.4 9.3 + - - +
97F PRO* 3.1 21.1 - - + +
99F ARG* 1.3 78.4 - - - +
101F TYR* 1.3 62.1 + - - +
103F ARG* 3.1 20.6 + - - +
104F GLU* 2.9 30.3 + - + +
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Residues in contact with TYR 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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290D ILE* 4.8 18.4 - - + -
291D ILE* 5.9 1.6 - - + -
294D ASN* 2.9 43.5 - - + +
297D ARG* 5.3 4.7 - - - +
97F PRO 3.0 17.0 + - - +
98F VAL* 3.9 4.5 - - - +
100F MET* 1.3 79.2 - - + +
102F MET* 1.3 65.2 + - + +
104F GLU* 3.2 8.6 + - + +
105F MET* 3.0 55.8 + - + +
384F LEU* 4.1 19.5 + - + +
387F VAL* 5.8 0.5 - - - +
388F ILE* 5.3 5.7 - - + +
402F LEU* 5.4 2.9 - - + -
405F ILE* 3.7 24.5 - - + +
406F GLN* 4.6 3.4 - - - -
409F ASN* 3.5 24.3 + - - -
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Residues in contact with MET 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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98F VAL* 2.8 36.6 + - + +
99F ARG* 3.1 13.0 + - - +
101F TYR* 1.3 75.3 - - + +
103F ARG* 1.3 58.4 + - + +
105F MET* 3.1 34.7 - - + +
106F GLY* 2.9 24.8 + - - -
388F ILE* 4.1 12.1 - - - -
401F PHE* 6.2 0.2 - - - -
53X G 3.2 47.0 + - + +
54X C 3.1 35.9 - - - +
55X G 4.5 14.6 - - - +
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Residues in contact with ARG 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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142D GLU* 5.5 9.2 + - - +
94F THR* 5.2 15.4 + - - +
99F ARG* 3.0 22.1 + - - +
100F MET* 3.5 20.2 + - - +
102F MET* 1.3 75.2 - - + +
104F GLU* 1.3 75.0 + - - +
106F GLY* 2.8 19.4 + - - +
107F THR* 3.0 15.5 + - - -
53X G 5.9 1.8 - - - +
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Residues in contact with GLU 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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141D PHE 4.6 10.6 - - - +
142D GLU* 5.3 7.4 - - - +
290D ILE* 4.7 21.5 - - + +
297D ARG* 4.5 20.4 + - - +
100F MET* 2.9 23.6 + - - +
101F TYR* 3.2 11.6 + - + +
103F ARG* 1.3 90.2 + - - +
105F MET* 1.3 63.4 + - - +
107F THR* 3.2 21.4 + - - -
108F VAL* 4.2 5.4 + - - +
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Residues in contact with MET 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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290D ILE* 5.7 0.8 - - - +
101F TYR* 3.0 35.0 + - + +
102F MET* 3.1 58.1 - - + +
104F GLU* 1.3 76.5 - - - +
106F GLY* 1.3 63.0 + - - +
107F THR 2.9 1.6 + - - -
108F VAL* 3.1 26.7 + - + +
384F LEU* 4.5 24.7 - - + +
385F ARG* 3.4 25.9 + - + +
388F ILE* 3.5 35.0 - - + -
53X G 5.1 9.0 - - + +
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Residues in contact with GLY 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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102F MET 2.9 13.5 + - - -
103F ARG* 2.8 16.9 + - - -
105F MET* 1.3 72.2 - - - +
107F THR* 1.3 60.8 + - - +
108F VAL 3.4 0.4 + - - -
109F GLU* 5.5 0.2 - - - -
385F ARG* 3.5 21.5 + - - -
53X G 3.8 20.3 - - - +
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Residues in contact with THR 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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103F ARG 3.0 10.5 + - - -
104F GLU* 3.5 17.1 + - - -
105F MET 2.9 1.4 + - - -
106F GLY* 1.3 79.8 - - - +
108F VAL* 1.3 68.9 + - + +
109F GLU* 3.3 5.2 + - - +
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Residues in contact with VAL 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE* 6.2 0.4 - - + -
104F GLU 4.9 3.4 - - - +
105F MET* 3.1 20.4 - - + +
107F THR* 1.3 81.5 - - + +
109F GLU* 1.3 59.6 + - - +
381F GLU* 3.0 54.5 - - + +
382F ALA* 5.4 0.4 - - - -
384F LEU* 5.0 2.2 - - + -
385F ARG* 2.0 34.4 + - + -
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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