Contacts of the helix formed by residues 106 - 117 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 4.0 17.0 - - + -
98A PRO* 5.0 5.4 - - + -
101A LEU 4.8 0.9 - - - +
102A THR* 2.9 31.3 + - + +
105A MET* 1.3 112.9 - - + +
107A MET* 1.3 65.8 + - - +
108A PRO* 3.3 2.7 - - - -
109A MET* 3.1 20.3 + - + +
110A LEU* 2.9 37.2 + - + +
142A PHE* 3.8 33.7 - - + -
157A ILE* 4.0 21.8 - - + -
264A ILE* 4.6 12.3 - - + -
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Residues in contact with MET 107 (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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102A THR* 3.1 6.4 + - - +
103A LYS* 3.4 19.7 - - + +
106A MET* 1.3 79.2 - - - +
108A PRO* 1.3 59.9 - - + +
110A LEU* 3.9 20.0 - - + -
111A ASN* 2.7 65.0 + - - +
114A MET* 4.3 5.2 - - + -
124A LEU* 4.3 3.4 - - - -
215B PHE* 3.7 21.3 - - + -
222B VAL* 3.6 53.8 - - + +
225B SER* 4.0 17.7 - - - +
226B ALA* 4.4 0.2 - - + -
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Residues in contact with PRO 108 (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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103A LYS 3.8 3.4 - - - +
104A ARG 3.7 23.3 - - - +
105A MET 4.4 1.8 - - - +
106A MET 3.5 4.5 - - - +
107A MET* 1.3 93.8 - - + +
109A MET* 1.3 62.6 + - - +
111A ASN* 3.9 4.8 - - + +
112A GLY* 3.0 20.3 + - - -
288A TYR* 3.9 19.2 + - + +
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Residues in contact with MET 109 (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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105A MET 4.2 18.1 + - - +
106A MET* 3.1 26.1 + - + +
108A PRO* 1.3 78.4 - - - +
110A LEU* 1.3 61.9 + - + +
112A GLY 3.3 0.9 + - - -
113A PHE* 2.9 25.3 + - - +
142A PHE* 4.8 4.3 - - + -
157A ILE* 4.5 8.1 - - + -
281A PHE* 6.0 2.0 - - + -
284A TYR* 3.4 19.2 - - + -
285A VAL* 3.8 26.0 - - + -
288A TYR* 3.8 40.6 + - + -
289A ASN* 3.5 26.5 - - - +
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Residues in contact with LEU 110 (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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95A ILE* 3.6 21.8 - - + -
97A THR* 5.0 3.6 - - + -
106A MET* 2.9 37.6 + - + +
107A MET* 3.8 26.9 - - + +
109A MET* 1.3 78.3 - - + +
111A ASN* 1.3 62.7 + - - +
113A PHE* 3.3 4.6 + - + +
114A MET* 3.0 35.2 + - + +
122A ILE* 4.9 11.2 - - + -
124A LEU* 4.1 17.3 - - + -
142A PHE* 5.9 1.8 - - + -
281A PHE* 3.5 33.0 - - + -
215B PHE* 5.3 2.0 - - + -
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Residues in contact with ASN 111 (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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107A MET* 2.7 44.6 + - - +
108A PRO* 4.0 4.6 - - + +
110A LEU* 1.3 72.7 - - - +
112A GLY* 1.3 57.3 + - - +
114A MET* 3.5 5.4 - - - +
115A SER* 3.0 30.7 + - - -
225B SER* 3.0 27.9 + - - -
226B ALA* 3.4 17.3 - - - +
229B GLU* 3.4 32.7 - - + +
231B LEU* 3.5 11.7 - - + +
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Residues in contact with GLY 112 (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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108A PRO 3.0 14.9 + - - -
109A MET 3.3 2.0 + - - -
111A ASN* 1.3 78.1 - - - +
113A PHE* 1.3 59.9 + - - +
115A SER* 3.4 7.7 - - - -
116A GLN* 3.1 21.3 + - - +
284A TYR* 3.1 22.2 + - - -
288A TYR* 5.6 0.9 - - - -
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Residues in contact with PHE 113 (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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93A ILE* 4.3 0.7 - - + -
109A MET 2.9 16.3 + - - +
110A LEU* 3.8 7.2 - - + +
111A ASN 3.3 0.2 - - - -
112A GLY* 1.3 74.4 - - - +
114A MET* 1.3 73.9 + - + +
116A GLN* 2.9 2.8 + - - -
117A TYR* 2.9 49.5 + + + -
120A ILE* 3.7 45.3 - - + -
122A ILE* 4.1 14.1 - - + -
280A LEU 3.9 1.3 - - - -
281A PHE* 3.4 54.5 - + + -
284A TYR* 3.5 34.9 + + + -
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Residues in contact with MET 114 (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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107A MET* 4.3 2.7 - - + -
110A LEU* 3.0 24.2 + - + +
111A ASN* 3.5 27.4 - - - +
113A PHE* 1.3 81.5 - - + +
115A SER* 1.3 57.8 + - - +
117A TYR 3.4 6.4 - - - +
118A PRO* 3.3 12.3 - - - +
120A ILE 5.2 4.3 - - - +
122A ILE* 4.1 22.2 - - + -
214B ARG* 2.6 44.5 + - - +
215B PHE* 3.7 51.6 - - + -
226B ALA* 4.2 4.0 - - + -
231B LEU* 4.0 16.8 - - + -
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Residues in contact with SER 115 (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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111A ASN 3.0 19.2 + - - -
112A GLY* 3.4 10.3 - - - -
114A MET* 1.3 79.3 - - - +
116A GLN* 1.3 58.5 + - - +
117A TYR 3.6 0.2 + - - -
118A PRO* 3.8 12.1 - - - +
214B ARG* 4.0 2.1 + - - +
231B LEU* 4.0 16.6 - - - +
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Residues in contact with GLN 116 (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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112A GLY 3.1 9.8 + - - +
113A PHE 2.9 8.5 + - - +
115A SER* 1.3 77.0 - - - +
117A TYR* 1.3 99.3 + - + +
118A PRO* 3.4 7.1 - - - +
119A GLU* 4.7 0.9 - - - +
284A TYR* 3.2 25.9 - - + -
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Residues in contact with TYR 117 (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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113A PHE* 2.9 47.2 + + + +
114A MET* 3.4 9.3 - - - +
116A GLN* 1.3 115.8 + - + +
118A PRO* 1.3 67.8 - - - +
119A GLU* 3.1 20.9 - - - +
120A ILE* 3.0 44.2 + - + +
280A LEU* 3.8 39.3 + - + +
284A TYR* 4.5 5.3 - + - +
214B ARG* 5.1 0.2 + - - -
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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