Contacts of the helix formed by residues 106 - 117 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E THR* 4.5 9.6 - - + -
98E PRO* 4.8 2.0 - - + -
102E THR* 2.9 33.4 + - + +
105E MET* 1.3 102.9 - - + +
107E MET* 1.3 66.4 + - - +
108E PRO* 3.4 2.5 - - - -
109E MET* 3.2 27.9 + - + +
110E LEU* 2.9 32.6 + - + +
142E PHE* 3.5 55.6 - - + -
157E ILE* 4.6 10.3 - - + -
264E ILE* 4.9 0.4 - - - -
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Residues in contact with MET 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PHE* 3.6 30.7 - - + -
222D VAL* 3.4 32.8 - - + +
225D SER* 3.3 25.6 - - - +
226D ALA* 4.3 1.1 - - + -
102E THR* 3.0 16.8 + - - +
103E LYS* 3.2 21.5 - - - +
106E MET* 1.3 75.8 - - - +
108E PRO* 1.3 56.0 - - + +
110E LEU* 3.5 23.1 - - + -
111E ASN* 2.7 68.8 + - - +
114E MET* 4.4 3.8 - - + -
124E LEU* 4.5 1.6 - - - -
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Residues in contact with PRO 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D GLU* 6.5 0.9 - - - -
103E LYS 3.7 9.6 - - - +
104E ARG* 3.8 18.6 - - - +
105E MET 4.4 2.7 - - - +
106E MET 3.5 4.3 - - - +
107E MET* 1.3 93.0 - - + +
109E MET* 1.3 56.3 + - - +
111E ASN* 4.0 6.7 - - + +
112E GLY* 3.1 22.0 + - - -
288E TYR* 3.5 23.6 + - + +
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Residues in contact with MET 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E MET 5.2 3.3 + - - +
106E MET* 3.2 38.3 + - + +
108E PRO* 1.3 76.9 - - - +
110E LEU* 1.3 81.5 + - + +
112E GLY* 3.2 1.2 + - - -
113E PHE* 2.9 18.7 + - - +
142E PHE* 4.5 1.1 - - + -
157E ILE* 5.5 1.6 - - + -
281E PHE* 4.5 2.9 - - - -
284E TYR* 3.3 18.3 - - + -
285E VAL* 3.5 44.2 - - + +
288E TYR* 3.6 48.8 + - + -
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Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PHE* 5.2 3.1 - - + -
95E ILE* 3.7 24.7 - - + -
97E THR* 4.8 1.1 - - + -
106E MET* 2.9 32.4 + - + +
107E MET* 3.5 24.2 - - + +
109E MET* 1.3 85.1 - - + +
111E ASN* 1.3 61.8 + - - +
113E PHE* 3.1 6.6 + - - +
114E MET* 3.0 35.2 + - + +
122E ILE* 5.4 6.1 - - + -
124E LEU* 3.5 31.6 - - + -
281E PHE* 3.7 24.5 - - + -
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Residues in contact with ASN 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D SER* 3.2 27.1 + - - -
226D ALA* 3.5 4.8 - - - -
229D GLU* 3.5 28.9 - - + +
231D LEU* 3.3 28.6 - - + +
107E MET* 2.7 46.6 + - - +
108E PRO* 4.0 6.2 - - + +
110E LEU* 1.3 72.8 - - - +
112E GLY* 1.3 61.8 + - - +
114E MET* 3.3 5.5 + - - +
115E SER* 3.0 25.5 + - - -
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Residues in contact with GLY 112 (chain E).
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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108E PRO 3.1 16.1 + - - -
109E MET 3.2 2.2 + - - -
111E ASN* 1.3 76.0 - - - +
113E PHE* 1.3 60.5 + - - +
115E SER* 3.3 9.2 + - - -
116E GLN* 3.1 23.0 + - - +
284E TYR* 3.1 20.8 + - - -
288E TYR* 5.3 1.3 - - - -
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Residues in contact with PHE 113 (chain E).
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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93E ILE* 4.6 0.4 - - + -
109E MET 2.9 13.8 + - - +
110E LEU* 3.4 10.5 - - - +
112E GLY* 1.3 76.2 - - - +
114E MET* 1.3 63.2 + - + +
116E GLN 3.3 1.0 + - - -
117E TYR* 2.9 57.6 + + - +
120E ILE* 3.8 43.3 - - + -
122E ILE* 4.4 10.1 - - + -
280E LEU* 3.6 9.6 - - + -
281E PHE* 3.4 56.5 - + + -
284E TYR* 3.4 34.4 + + + -
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Residues in contact with MET 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ARG* 3.0 35.6 + - + +
215D PHE* 3.8 50.3 - - + -
231D LEU* 3.7 14.1 - - + -
107E MET* 4.4 2.5 - - + -
110E LEU* 3.0 23.5 + - + +
111E ASN* 3.4 26.9 - - - +
113E PHE* 1.3 76.8 - - + +
115E SER* 1.3 68.3 + - - +
117E TYR 3.3 20.7 - - - +
118E PRO* 3.6 0.3 - - - +
120E ILE* 5.2 7.0 - - + +
122E ILE* 3.9 25.4 - - + -
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Residues in contact with SER 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ARG* 3.6 10.6 + - - +
229D GLU 6.0 0.4 - - - -
231D LEU* 3.6 17.8 - - - +
111E ASN 3.0 11.5 + - - -
112E GLY* 3.3 13.0 + - - -
114E MET* 1.3 77.9 - - - +
116E GLN* 1.4 63.3 + - - +
118E PRO* 3.8 13.3 - - - +
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Residues in contact with GLN 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E GLY 3.1 13.9 + - - +
113E PHE* 3.7 4.9 - - - +
115E SER* 1.4 81.7 + - - +
117E TYR* 1.3 96.6 + - + +
118E PRO* 3.3 8.3 - - - +
284E TYR* 3.8 21.6 + - + -
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Residues in contact with TYR 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ALA 5.4 4.0 - - - -
113E PHE* 2.9 52.1 + + + +
114E MET* 3.3 8.4 + - - +
116E GLN* 1.3 111.7 + - + +
118E PRO* 1.3 60.1 - - - +
119E GLU 2.8 12.7 + - - -
120E ILE* 3.0 40.1 + - + +
280E LEU* 3.8 35.9 + - + +
284E TYR* 4.7 5.1 - + - +
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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