Contacts of the helix formed by residues 106 - 117 (chain F) in PDB entry 5FHK
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 MET 106 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F THR* 4.0 17.3 - - + -
98F PRO* 4.8 1.3 - - + -
102F THR* 3.0 30.9 + - + +
105F MET* 1.3 99.1 - - + +
107F MET* 1.3 67.0 + - - +
108F PRO* 3.4 1.6 - - - -
109F MET* 3.1 25.1 + - + +
110F LEU* 2.9 37.6 + - + +
142F PHE* 3.5 59.9 - - + -
157F ILE* 4.6 5.4 - - - -
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Residues in contact with MET 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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215C PHE* 3.6 17.5 - - + -
222C VAL* 3.3 47.6 - - + +
225C SER* 3.5 22.7 - - - +
226C ALA* 4.1 2.0 - - + -
102F THR* 3.0 16.5 + - - +
103F LYS* 3.1 28.3 - - - +
106F MET* 1.3 75.8 - - - +
108F PRO* 1.3 57.1 - - + +
110F LEU* 2.9 20.9 + - + +
111F ASN* 2.7 63.1 + - - +
114F MET* 4.5 4.0 - - + -
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Residues in contact with PRO 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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229C GLU* 6.3 0.4 - - + -
103F LYS 3.8 4.7 - - - +
104F ARG* 3.7 22.4 - - - +
105F MET 4.4 2.0 - - - +
106F MET 3.6 4.0 - - - +
107F MET* 1.3 91.4 - - + +
109F MET* 1.3 60.3 + - - +
111F ASN* 4.0 7.6 - - + +
112F GLY* 3.1 19.6 + - - -
288F TYR* 3.5 18.6 + - + +
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Residues in contact with MET 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 MET 5.0 6.0 + - - +
106F MET* 3.1 38.2 + - + +
108F PRO* 1.3 80.9 - - - +
110F LEU* 1.3 61.6 + - + +
112F GLY 3.4 0.7 + - - -
113F PHE* 3.0 23.8 + - + +
142F PHE* 4.4 4.5 - - + -
157F ILE* 4.6 9.6 - - + -
281F PHE* 6.1 0.4 - - + -
284F TYR* 3.3 13.5 - - + -
285F VAL* 3.7 44.0 - - + +
288F TYR* 3.7 47.1 + - + -
289F ASN 5.6 2.7 - - - +
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Residues in contact with LEU 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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215C PHE* 4.8 5.6 - - + -
95F ILE* 3.8 15.7 - - + -
106F MET* 2.9 31.2 + - + +
107F MET* 2.9 22.8 + - - +
109F MET* 1.3 77.5 - - + +
111F ASN* 1.3 66.6 + - - +
113F PHE* 3.2 3.8 + - - +
114F MET* 3.0 37.6 + - + +
122F ILE* 4.0 6.7 - - + -
124F LEU* 3.5 31.9 - - + -
281F PHE* 3.6 37.0 - - + -
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Residues in contact with ASN 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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225C SER* 2.9 28.9 + - - -
226C ALA* 3.2 21.2 - - - +
229C GLU* 3.3 36.0 - - + +
231C LEU* 3.4 17.2 - - + +
107F MET* 2.7 35.4 + - - +
108F PRO* 4.0 6.2 - - + +
110F LEU* 1.3 71.9 - - - +
112F GLY* 1.3 56.9 + - - +
114F MET* 3.8 1.9 - - - +
115F SER* 3.0 30.0 + - - -
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Residues in contact with GLY 112 (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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108F PRO 3.1 15.9 + - - -
109F MET 3.4 1.5 + - - -
111F ASN* 1.3 76.6 - - - +
113F PHE* 1.3 60.2 + - - +
115F SER* 3.2 7.0 + - - -
116F GLN* 3.1 23.2 + - - +
284F TYR* 3.1 21.1 + - - -
288F TYR* 5.3 0.7 - - - -
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Residues in contact with PHE 113 (chain F).
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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93F ILE* 4.4 3.6 - - + -
109F MET* 3.0 12.6 + - + +
110F LEU* 3.2 5.6 + - - +
112F GLY* 1.3 75.2 - - - +
114F MET* 1.3 65.0 + - + +
116F GLN 3.2 1.6 + - - -
117F TYR* 3.0 59.1 + + + +
120F ILE* 3.9 38.8 - - + -
122F ILE* 4.1 16.4 - - + -
277F LYS 4.5 0.7 - - - -
280F LEU* 4.0 1.6 - - + -
281F PHE* 3.4 55.6 - + + -
284F TYR* 3.3 40.4 + - + -
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Residues in contact with MET 114 (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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214C ARG* 2.8 38.3 + - - +
215C PHE* 3.4 52.9 - - + -
226C ALA* 4.6 0.2 - - + -
231C LEU* 3.8 18.6 - - + -
107F MET* 4.5 0.7 - - + -
110F LEU* 3.0 26.6 + - + +
111F ASN* 3.8 22.7 - - - +
113F PHE* 1.3 79.1 - - + +
115F SER* 1.3 64.1 + - - +
116F GLN 3.3 0.5 + - - -
117F TYR 3.4 17.3 + - - +
120F ILE 4.9 6.5 - - - +
122F ILE* 3.8 26.2 - - + -
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Residues in contact with SER 115 (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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214C ARG* 4.0 7.1 + - - +
229C GLU 6.0 0.7 - - - -
231C LEU* 4.1 11.6 - - - +
111F ASN 3.0 19.0 + - - -
112F GLY* 3.6 8.5 - - - -
113F PHE 3.2 0.4 - - - -
114F MET* 1.3 78.4 - - - +
116F GLN* 1.3 60.2 + - - +
117F TYR 3.7 0.2 + - - -
118F PRO* 4.0 11.4 - - - +
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Residues in contact with GLN 116 (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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112F GLY 3.1 15.0 + - - +
113F PHE* 3.7 5.2 - - - +
114F MET 3.2 0.2 - - - -
115F SER* 1.3 78.9 - - - +
117F TYR* 1.3 98.5 + - + +
118F PRO* 3.3 9.9 - - - +
284F TYR* 3.6 22.0 - - - -
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Residues in contact with TYR 117 (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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214C ARG* 5.3 0.2 + - - -
89F ALA 5.3 1.6 - - - -
113F PHE* 3.0 48.5 + + + +
114F MET* 3.4 10.2 - - - +
116F GLN* 1.3 111.5 + - + +
118F PRO* 1.3 66.3 - - - +
119F GLU 3.0 4.9 + - - -
120F ILE* 3.2 44.7 + - + +
280F LEU* 3.9 39.4 + - + +
284F TYR* 4.6 5.9 - + - +
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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