Contacts of the helix formed by residues 106 - 117 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D THR* 4.5 10.3 - - + -
98D PRO* 5.1 1.3 - - + -
102D THR* 2.9 32.4 + - + +
105D MET* 1.3 130.1 - - + +
107D MET* 1.3 61.8 + - - +
108D PRO* 3.4 2.2 - - - -
109D MET* 3.1 18.3 + - + +
110D LEU* 2.8 40.3 + - + +
142D PHE* 4.0 37.2 - - - -
157D ILE* 4.4 16.8 - - + -
264D ILE* 5.0 0.9 - - + -
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Residues in contact with MET 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR* 3.1 17.5 + - - +
103D LYS* 3.2 26.7 - - - +
106D MET* 1.3 75.4 - - - +
108D PRO* 1.4 56.0 - - + +
110D LEU* 4.0 25.6 - - + -
111D ASN* 2.6 66.0 + - - +
114D MET* 4.5 1.8 - - + -
124D LEU* 4.9 0.2 - - - -
215E PHE* 3.8 14.6 - - + -
222E VAL* 3.1 43.7 - - + +
225E SER* 3.6 21.1 - - - +
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Residues in contact with PRO 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LYS 3.7 9.6 - - - +
104D ARG* 3.8 16.8 - - - +
105D MET 4.4 3.1 - - - +
106D MET 3.6 3.6 - - - +
107D MET* 1.4 91.8 - - + +
109D MET* 1.3 56.2 + - - +
111D ASN* 3.9 6.4 - - + +
112D GLY* 3.0 25.3 + - - -
288D TYR* 3.7 20.9 + - + +
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Residues in contact with MET 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET 5.2 3.9 + - - +
106D MET* 3.1 24.4 + - + +
108D PRO* 1.3 80.4 - - - +
110D LEU* 1.3 82.1 + - + +
112D GLY 3.2 1.0 + - - -
113D PHE* 2.9 24.8 + - - +
142D PHE* 4.1 16.8 - - + -
157D ILE* 5.8 0.7 - - + -
281D PHE* 4.4 2.9 - - - -
284D TYR* 3.4 19.3 - - + -
285D VAL* 3.6 38.1 - - + -
288D TYR* 3.7 44.2 + - + -
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 4.0 12.3 - - + -
97D THR* 4.8 2.2 - - + -
106D MET* 2.8 33.0 + - + +
107D MET* 3.7 27.1 - - + +
109D MET* 1.3 81.1 - - + +
111D ASN* 1.3 58.0 + - - +
113D PHE* 3.3 4.9 + - - +
114D MET* 3.0 39.5 + - + +
122D ILE* 4.6 5.8 - - + +
124D LEU* 3.5 31.9 - - + -
142D PHE* 5.2 1.6 - - + -
281D PHE* 3.6 34.5 - - + -
215E PHE* 5.1 4.5 - - + -
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Residues in contact with ASN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D MET* 2.6 42.3 + - - +
108D PRO* 4.0 5.4 - - + +
110D LEU* 1.3 68.8 - - - +
112D GLY* 1.3 64.9 + - - +
114D MET* 3.6 2.3 - - - +
115D SER* 3.0 25.0 + - - -
225E SER* 3.0 27.9 + - - -
226E ALA* 3.3 20.9 - - - +
229E GLU* 3.5 32.2 - - + +
231E LEU* 3.4 16.1 - - + +
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Residues in contact with GLY 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PRO 3.0 16.3 + - - -
109D MET 3.7 1.3 - - - -
111D ASN* 1.3 78.9 - - - +
113D PHE* 1.3 61.2 + - - +
115D SER* 3.2 7.8 + - - -
116D GLN* 3.0 21.7 + - - +
284D TYR* 3.1 21.3 + - - -
288D TYR* 5.3 0.9 - - - -
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 4.4 0.9 - - + -
109D MET* 2.9 14.0 + - - +
110D LEU* 3.5 9.4 - - - +
112D GLY* 1.3 74.4 - - - +
114D MET* 1.3 67.1 + - + +
116D GLN 3.0 2.6 + - - -
117D TYR* 2.9 49.7 + + + -
120D ILE* 3.8 46.4 - - + -
122D ILE* 3.9 19.5 - - + -
280D LEU 3.9 1.1 - - - -
281D PHE* 3.4 54.3 - + + -
284D TYR* 3.4 36.2 + + + -
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Residues in contact with MET 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D MET* 4.5 3.1 - - + -
110D LEU* 3.0 27.8 + - + +
111D ASN* 3.6 22.0 - - - +
113D PHE* 1.3 78.1 - - + +
115D SER* 1.3 62.3 + - - +
117D TYR 3.2 19.9 - - - +
120D ILE 4.8 6.1 - - - +
122D ILE* 3.7 26.9 - - + -
214E ARG* 2.9 35.9 + - - +
215E PHE* 3.7 50.5 - - + -
231E LEU* 3.7 18.4 - - + -
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Residues in contact with SER 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASN 3.0 14.6 + - - -
112D GLY* 3.3 12.3 - - - -
114D MET* 1.3 79.4 - - - +
116D GLN* 1.4 61.7 + - - +
118D PRO* 3.7 13.9 - - - +
214E ARG* 4.1 2.6 + - - +
229E GLU 5.6 1.3 + - - -
231E LEU* 4.0 17.7 - - - +
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D GLY 3.0 11.9 + - - +
113D PHE 3.0 7.2 + - - +
115D SER* 1.4 75.8 - - - +
117D TYR* 1.3 100.2 + - + +
118D PRO* 3.4 7.4 - - - +
284D TYR* 3.3 26.9 + - + -
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Residues in contact with TYR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ALA* 4.8 2.0 - - + -
113D PHE* 2.9 47.2 + + + +
114D MET* 3.2 9.7 + - - +
116D GLN* 1.3 117.7 + - + +
118D PRO* 1.3 66.9 - - - +
119D GLU* 3.2 22.0 - - - +
120D ILE* 3.0 33.5 + - + +
280D LEU* 4.0 43.3 + - + +
284D TYR* 4.5 5.1 - + - +
214E ARG* 5.3 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