Contacts of the helix formed by residues 111 - 122 (chain P) in PDB entry 3FKS
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 GLY 111 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78P THR* 4.1 2.5 - - - -
79P SER 3.2 22.7 - - - -
80P ASP* 4.0 6.5 - - - -
109P THR* 4.5 2.1 - - - -
110P ILE* 1.3 76.0 - - - +
112P ASP* 1.3 64.0 + - - -
113P LYS 3.3 2.7 - - - -
114P ILE* 2.9 28.5 - - - +
115P LYS* 3.5 4.2 + - - +
129P SER* 5.2 0.6 + - - -
130P ILE 3.3 11.6 + - - +
131P ASN* 5.2 0.6 - - - +
132P GLY 5.7 0.4 - - - +
133P ILE* 5.8 1.1 - - - +
134P GLY 6.0 0.7 - - - -
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Residues in contact with ASP 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411L ASP* 4.8 11.1 - - - +
79P SER 3.5 1.0 + - - -
80P ASP* 3.3 17.7 + - + +
111P GLY* 1.3 68.0 - - - -
113P LYS* 1.3 60.8 + - + +
114P ILE 2.9 10.9 + - - -
115P LYS* 3.0 47.2 + - - +
116P MET* 3.2 16.0 + - + +
129P SER* 4.0 1.6 + - - -
130P ILE 4.0 6.8 - - - +
131P ASN* 3.0 37.4 + - - +
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Residues in contact with LYS 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408L PHE 5.3 7.5 + - - +
409L GLY 4.3 7.2 - - - +
410L SER* 5.5 3.4 - - - +
79P SER 3.5 2.1 + - - +
80P ASP* 3.1 30.7 - - - +
81P LYS 4.6 0.7 - - - -
82P GLY* 3.7 23.0 - - - +
88P HIS* 3.1 47.9 + - + +
111P GLY 3.3 1.2 - - - -
112P ASP* 1.3 76.8 - - + +
114P ILE* 1.3 57.2 + - - +
116P MET* 3.4 38.0 - - - +
117P GLN* 3.1 21.6 - - - +
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Residues in contact with ILE 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P ALA* 4.0 20.9 - - + -
78P THR* 3.1 27.3 + - + +
88P HIS* 4.1 9.0 - - - +
91P LEU* 4.1 16.4 - - + -
92P ALA* 3.5 39.0 - - + +
109P THR* 3.6 24.2 - - + -
110P ILE 4.1 4.9 - - - +
111P GLY 2.9 22.4 + - - +
112P ASP 2.9 0.6 - - - -
113P LYS* 1.3 77.5 - - - +
115P LYS* 1.3 62.3 + - - +
116P MET 2.9 5.9 + - - -
117P GLN* 3.5 4.2 + - - +
118P LEU* 3.2 29.2 + - + +
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Residues in contact with LYS 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411L ASP* 5.9 3.2 + - - +
109P THR* 4.0 11.4 - - - +
111P GLY 4.2 3.8 - - - +
112P ASP* 3.0 41.9 + - - +
114P ILE* 1.3 82.2 - - - +
116P MET* 1.3 56.9 + - - +
118P LEU* 4.4 0.2 - - - -
119P LEU* 2.8 56.4 + - + +
126P ILE* 4.1 20.0 - - + -
129P SER* 3.7 24.2 + - - +
131P ASN* 5.5 1.2 - - - +
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Residues in contact with MET 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409L GLY* 3.3 30.5 - - - +
410L SER* 5.5 0.2 - - - -
397O SER* 5.8 5.4 - - - +
398O GLU* 5.5 9.2 - - + +
112P ASP* 3.2 16.0 + - + +
113P LYS* 3.4 35.2 - - - -
114P ILE 2.9 1.2 - - - -
115P LYS* 1.3 77.9 - - - +
117P GLN* 1.3 80.5 + - - +
118P LEU 3.1 5.5 + - - -
119P LEU* 4.2 3.2 - - - +
120P ARG* 3.4 27.1 + - - +
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Residues in contact with GLN 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398O GLU* 3.5 37.9 + - + +
88P HIS* 2.9 25.6 - - - +
89P SER* 4.9 7.6 - - - +
92P ALA* 3.3 29.1 - - + +
93P LYS* 6.2 1.6 - - + -
96P ARG* 5.6 0.7 - - - +
113P LYS* 3.1 21.6 + - - +
114P ILE* 3.5 1.4 + - - -
116P MET* 1.3 94.8 - - - +
118P LEU* 1.3 55.6 + - + +
120P ARG* 4.2 17.5 + - - +
121P THR* 2.7 30.0 + - - +
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Residues in contact with LEU 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P ALA* 4.5 8.1 - - + -
92P ALA* 3.9 20.0 - - + +
95P VAL* 3.8 32.5 - - + -
96P ARG* 4.8 2.7 - - + +
107P ILE* 4.7 9.2 - - + -
109P THR* 3.6 30.1 - - + -
114P ILE* 3.2 17.4 + - + +
116P MET 3.1 0.6 - - - -
117P GLN* 1.3 84.3 - - - +
119P LEU* 1.3 62.5 + - - +
120P ARG 3.0 1.3 - - - -
121P THR* 4.0 4.9 - - - +
122P HIS* 2.8 46.0 + - + +
126P ILE* 3.8 18.4 - - + -
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Residues in contact with LEU 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P LYS* 2.8 54.2 + - + +
116P MET* 3.7 4.7 + - - +
118P LEU* 1.3 71.9 - - - +
120P ARG* 1.3 58.4 + - + +
123P PRO* 3.2 48.6 - - + +
126P ILE* 4.4 6.0 - - + +
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Residues in contact with ARG 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398O GLU* 4.0 40.9 + - - +
399O GLN* 5.6 4.5 - - - +
116P MET 3.4 18.7 + - - +
117P GLN* 4.2 20.7 + - - +
118P LEU 3.0 1.4 - - - -
119P LEU* 1.3 78.7 - - + +
121P THR* 1.3 79.4 + - + +
123P PRO* 3.2 13.5 - - - +
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Residues in contact with THR 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P ARG* 4.4 10.0 - - + +
117P GLN 2.7 25.0 + - - +
118P LEU* 3.3 0.9 + - - -
120P ARG* 1.3 98.1 - - + +
122P HIS* 1.3 89.7 + - - +
123P PRO* 3.4 4.1 - - - +
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Residues in contact with HIS 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P VAL* 5.6 2.2 - - + -
96P ARG* 3.6 41.0 + - + +
107P ILE* 6.2 1.1 - - + -
118P LEU* 2.8 30.7 + - + +
121P THR* 1.3 97.9 + - - +
123P PRO* 1.3 64.3 - - - +
124P ASN 3.1 4.3 + - - -
125P ASN* 3.1 45.5 + - + +
126P ILE* 4.3 4.7 + - - +
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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