Contacts of the helix formed by residues 106 - 117 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B THR* 4.0 16.6 - - + -
98B PRO* 4.4 7.9 - - + -
101B LEU* 4.7 1.1 - - + +
102B THR* 2.9 27.1 + - + +
105B MET* 1.3 88.9 - - + +
107B MET* 1.3 62.1 + - - +
108B PRO 3.5 0.4 - - - -
109B MET* 3.1 36.7 + - + +
110B LEU* 2.9 42.4 + - + +
142B PHE* 3.5 48.2 - - + -
157B ILE* 4.6 9.0 - - - -
264B ILE* 5.7 2.0 - - - -
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Residues in contact with MET 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 3.8 25.6 - - + -
222A VAL* 3.6 42.0 - - + +
225A SER* 3.8 16.6 - - - +
226A ALA* 4.4 0.4 - - + -
102B THR* 3.1 17.0 + - - +
103B LYS* 3.4 23.1 - - + +
106B MET* 1.3 75.3 - - - +
108B PRO* 1.3 58.3 - - + +
110B LEU* 3.0 19.3 + - + +
111B ASN* 2.6 66.6 + - - +
114B MET* 4.5 0.9 - - + -
124B LEU* 4.4 4.3 - - - -
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Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLU* 5.1 1.8 - - - +
103B LYS 3.7 9.6 - - - +
104B ARG 3.9 15.7 - - - +
105B MET 4.1 4.9 - - - +
106B MET 3.6 3.1 - - - -
107B MET* 1.3 92.2 - - + +
109B MET* 1.3 61.5 + - - +
111B ASN* 4.5 4.7 - - + +
112B GLY* 2.9 19.2 + - - -
288B TYR* 3.3 18.9 + - + +
132D GLN* 3.0 18.7 + - - +
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Residues in contact with MET 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET 4.8 5.3 + - - +
106B MET* 3.1 46.7 + - + +
108B PRO* 1.3 81.7 - - - +
110B LEU* 1.3 70.7 + - + +
112B GLY 3.3 0.2 + - - -
113B PHE* 3.0 19.1 + - - +
142B PHE* 4.1 4.0 - - + -
157B ILE* 5.0 5.8 - - + -
281B PHE* 6.2 0.2 - - + -
284B TYR* 3.4 19.8 - - + -
285B VAL* 3.7 44.6 - - + +
288B TYR* 3.6 45.8 + - + -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 5.2 1.3 - - + -
95B ILE* 3.8 13.5 - - + -
97B THR* 4.7 0.2 - - + -
106B MET* 2.9 39.6 + - + +
107B MET* 3.7 15.5 - - + +
109B MET* 1.3 82.5 - - + +
111B ASN* 1.3 67.4 + - - +
113B PHE* 3.2 4.1 + - - +
114B MET* 2.9 36.9 + - + +
122B ILE* 4.5 7.1 - - + +
124B LEU* 3.5 32.3 - - + -
281B PHE* 3.5 37.2 - - + -
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER* 3.1 28.1 + - - -
226A ALA* 3.3 28.5 - - - +
229A GLU* 3.7 36.6 + - + +
231A LEU* 3.4 13.2 - - + +
107B MET* 2.6 35.2 + - - +
108B PRO* 3.9 4.7 - - - +
110B LEU* 1.3 71.9 - - - +
112B GLY* 1.3 63.1 + - - +
114B MET* 3.7 2.8 - - - +
115B SER* 3.0 26.1 + - - -
132D GLN* 4.1 0.9 - - - +
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PRO 2.9 15.5 + - - -
109B MET 3.6 2.0 - - - -
111B ASN* 1.3 77.7 - - - +
113B PHE* 1.3 59.7 + - - +
115B SER* 3.3 7.0 + - - -
116B GLN* 3.1 21.3 + - - +
284B TYR* 3.1 21.4 + - - -
129D ASN* 5.3 3.3 + - - -
132D GLN* 3.5 16.2 - - - +
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 4.2 4.5 - - + -
109B MET 3.0 13.4 + - - +
110B LEU* 3.2 9.8 + - - +
112B GLY* 1.3 77.1 - - - +
114B MET* 1.3 66.5 + - + +
116B GLN* 3.1 2.5 + - - -
117B TYR* 3.0 53.4 + + - +
120B ILE* 4.0 38.6 - - + -
122B ILE* 4.3 12.3 - - + -
277B LYS 4.5 0.4 - - - -
280B LEU* 3.9 4.3 - - + -
281B PHE* 3.4 56.3 - + + -
284B TYR* 3.4 34.2 + + + -
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Residues in contact with MET 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ARG* 2.8 37.4 + - - +
215A PHE* 3.6 53.8 - - + -
226A ALA* 4.4 0.7 - - + -
231A LEU* 3.9 17.7 - - + -
107B MET* 4.5 2.2 - - + -
110B LEU* 2.9 27.3 + - + +
111B ASN* 3.7 22.7 - - - +
113B PHE* 1.3 79.4 - - + +
115B SER* 1.3 62.2 + - - +
117B TYR 3.3 20.7 + - - +
120B ILE* 4.8 8.3 - - - +
122B ILE* 4.1 21.8 - - + -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ARG* 3.8 6.1 + - - +
229A GLU* 5.7 5.4 - - - -
231A LEU* 3.6 18.1 - - - +
111B ASN 3.0 18.9 + - - -
112B GLY* 3.6 7.2 - - - -
114B MET* 1.3 76.9 - - - +
116B GLN* 1.3 61.3 + - - +
118B PRO* 4.4 7.3 - - - +
131D ASP* 5.3 5.5 + - - +
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLY 3.1 11.0 + - - +
113B PHE* 3.1 9.7 + - - +
115B SER* 1.3 79.2 - - - +
117B TYR* 1.3 94.1 + - + +
118B PRO* 3.4 8.1 - - - +
284B TYR* 4.0 23.7 + - - -
129D ASN* 5.2 12.1 + - - +
192D HIS* 6.0 2.8 + - - -
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.0 50.5 + + + +
114B MET* 3.3 8.8 + - - +
116B GLN* 1.3 112.3 + - + +
118B PRO* 1.3 63.6 - - - +
119B GLU* 2.9 24.8 + - - +
120B ILE* 3.1 29.6 + - + +
280B LEU* 3.5 48.8 + - + +
284B TYR* 4.5 4.5 - + - +
192D HIS* 5.0 8.8 - - - -
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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