Contacts of the helix formed by residues 85 - 96 (chain A) in PDB entry 2FK8
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A CYS 3.3 9.4 + - - -
83A GLY 3.4 0.6 - - - -
84A TRP* 1.3 76.6 - - - +
86A THR* 1.3 62.7 + - - +
87A THR 3.4 3.1 - - - -
88A MET* 3.3 18.4 + - - +
89A ARG* 3.1 24.3 + - - +
112A CYS* 3.4 16.0 - - - -
115A VAL* 4.0 13.5 - - - +
116A LEU* 4.9 1.1 - - - +
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 3.0 46.8 + - + +
41A THR* 4.3 10.3 - - - +
58A GLN 6.3 0.4 - - - -
59A TYR* 4.0 25.6 - - + +
62A VAL* 4.7 9.6 - - + -
82A CYS 4.8 0.6 + - - -
84A TRP 3.6 3.6 + - - -
85A GLY* 1.3 76.8 - - - +
87A THR* 1.3 65.0 + - - +
89A ARG* 3.4 18.4 + - - +
90A ARG* 3.0 22.4 + - + +
115A VAL* 5.1 0.4 - - - +
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 6.0 1.2 - - - +
61A LYS* 5.6 0.3 - - - -
62A VAL* 3.7 34.2 - - + +
66A LEU* 4.3 9.8 - - + +
77A LEU* 5.4 1.1 - - + -
79A ASP* 3.6 20.6 - - - +
82A CYS 5.4 3.1 + - - -
85A GLY 3.4 0.4 - - - -
86A THR* 1.3 78.6 - - - +
88A MET* 1.3 60.1 + - - +
90A ARG* 3.7 2.4 - - - +
91A ALA* 3.0 26.9 + - - +
143A VAL* 4.1 20.6 - - + -
145A ILE* 4.0 20.2 - - + +
302A SAM 5.1 10.4 + - - -
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 5.5 2.9 - - + +
79A ASP* 3.8 21.3 + - + +
82A CYS* 3.7 27.1 - - + -
85A GLY* 3.3 23.1 + - - +
86A THR 3.3 0.6 - - - -
87A THR* 1.3 76.4 - - - +
89A ARG* 1.3 65.3 + - - +
91A ALA* 3.2 6.0 + - - +
92A VAL* 3.0 27.8 + - - +
99A VAL* 3.8 20.3 - - + +
100A ILE 4.0 3.1 - - - +
101A GLY* 3.4 33.7 - - - -
112A CYS* 4.0 5.8 - - + -
116A LEU* 3.7 35.7 - - + -
126A GLN 4.5 0.2 - - - +
127A VAL* 4.7 0.4 - - + -
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 4.8 10.7 + - - -
85A GLY 3.1 16.2 + - - +
86A THR* 3.9 15.8 + - - +
88A MET* 1.3 76.7 - - - +
90A ARG* 1.3 62.1 + - - +
92A VAL* 3.4 1.9 + - - +
93A GLU* 3.0 55.6 + - - +
115A VAL* 3.7 37.4 + - + +
116A LEU* 4.5 0.6 - - - +
118A SER* 5.5 2.8 + - - -
119A ILE* 3.8 29.6 - - + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.7 45.9 - - + +
62A VAL* 3.8 19.7 - - + -
63A ASP* 2.9 46.1 + - - +
66A LEU* 4.1 2.5 - - + -
86A THR* 3.0 19.0 + - + +
87A THR 3.7 4.0 - - - +
89A ARG* 1.3 77.6 - - - +
91A ALA* 1.3 56.5 + - - +
93A GLU* 3.4 11.6 + - - +
94A ARG* 2.9 49.8 + - - +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.8 16.4 - - + +
71A LEU* 5.2 0.4 - - + -
77A LEU* 3.5 31.6 - - + -
87A THR 3.0 12.6 + - - +
88A MET 3.2 8.9 + - - +
90A ARG* 1.3 74.0 - - - +
92A VAL* 1.3 59.6 + - - +
95A PHE* 2.8 40.1 + - + +
96A ASP 3.6 0.7 + - - -
97A VAL* 3.7 11.2 - - + +
99A VAL* 4.3 2.0 - - + -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A MET 3.0 15.5 + - - +
89A ARG 3.4 5.4 + - - +
91A ALA* 1.3 74.6 - - - +
93A GLU* 1.3 59.7 + - - +
96A ASP* 2.9 26.2 + - - -
97A VAL 3.4 25.6 - - - +
99A VAL* 3.6 24.9 - - + -
119A ILE* 4.0 15.7 - - + -
121A THR* 3.7 37.9 - - + +
123A ARG* 4.6 2.5 - - + -
125A ARG* 4.2 9.4 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ARG* 3.0 44.8 + - + +
90A ARG* 3.9 11.0 + - - +
92A VAL* 1.3 75.9 - - - +
94A ARG* 1.3 62.6 + - + +
96A ASP* 4.6 1.0 + - - +
119A ILE* 4.6 17.7 - - + +
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 2.7 52.8 + - - +
67A ASP* 2.9 32.0 + - - -
90A ARG* 2.9 43.7 + - - +
93A GLU* 1.3 77.5 - - + +
95A PHE* 1.3 96.0 + - + +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.6 36.8 - - + -
67A ASP* 3.6 11.9 - - - -
71A LEU* 4.0 37.2 - - + +
73A PRO* 3.5 20.9 - - - +
91A ALA* 2.8 26.4 + - - +
94A ARG* 1.3 119.0 - - + +
96A ASP* 1.3 73.7 + - - +
97A VAL* 3.3 17.9 + - + +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 3.9 13.5 - - + +
74A GLY 2.8 21.8 + - - -
91A ALA 3.6 0.2 + - - -
92A VAL 2.9 18.2 + - - -
93A GLU 4.6 0.8 + - - +
94A ARG 3.7 1.0 - - - -
95A PHE* 1.3 78.3 - - - +
97A VAL* 1.3 58.6 + - - +
121A THR* 4.5 3.8 + - - -
123A ARG* 2.8 49.8 + - - +
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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