Contacts of the helix formed by residues 101 - 106 (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 LEU 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B PRO* 3.4 28.5 + - + -
100B ASN* 1.3 84.3 - - + +
102B THR* 1.3 64.1 + - - +
103B LYS 3.4 2.0 + - - -
104B ARG* 3.6 3.1 + - - +
105B MET* 2.9 37.8 + - + +
106B MET* 5.1 1.3 - - + -
144B VAL* 4.5 11.9 - - + -
160B VAL* 4.4 12.8 - - + -
237B PRO* 4.1 32.1 - - + -
239B VAL* 4.6 9.4 - - + -
240B MET* 4.2 11.9 - - + -
264B ILE* 3.9 26.0 - - + -
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Residues in contact with THR 102 (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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222A VAL* 3.9 20.2 - - + -
97B THR* 2.6 31.2 + - - +
98B PRO 2.4 23.4 + - - -
99B TYR 4.3 2.9 + - - -
100B ASN 3.4 3.0 - - - -
101B LEU* 1.3 77.2 - - - +
103B LYS* 1.3 63.8 + - - +
106B MET* 2.9 32.3 + - + -
107B MET* 3.1 11.4 + - - +
124B LEU* 4.3 13.7 - - + -
126B THR* 3.6 17.1 - - + +
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Residues in contact with LYS 103 (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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221A ASN* 3.8 34.9 - - + +
222A VAL* 4.1 21.0 - - + +
224A ARG* 3.4 30.7 - - - +
225A SER* 4.6 7.0 - - - -
244A TYR* 5.6 0.2 + - - -
100B ASN 4.8 3.1 + - - +
101B LEU 3.4 0.4 - - - -
102B THR* 1.3 81.4 - - - +
104B ARG* 1.3 66.1 + - - +
107B MET* 3.4 28.2 + - + +
108B PRO* 3.7 3.8 - - - +
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Residues in contact with ARG 104 (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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100B ASN 5.5 1.0 + - - +
101B LEU* 3.6 4.7 + - - +
103B LYS* 1.3 80.6 - - - +
105B MET* 1.3 60.6 + - + +
108B PRO* 3.9 13.0 - - - +
239B VAL* 3.7 33.7 + - + +
240B MET* 3.0 45.2 + - + +
241B ILE 4.4 0.2 - - - +
242B LYS* 4.6 3.2 - - - +
243B GLU* 2.7 37.9 + - - +
244B TYR* 5.3 1.4 - - - -
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Residues in contact with MET 105 (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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98B PRO* 6.3 0.7 - - - -
101B LEU* 2.9 28.7 + - + +
104B ARG* 1.3 80.6 - - + +
106B MET* 1.3 71.9 + - + +
107B MET 3.7 0.2 - - - -
108B PRO* 4.1 5.7 - - - +
109B MET* 4.8 6.6 + - - +
157B ILE* 6.2 2.2 - - + -
158B GLY* 6.0 2.9 - - - -
159B SER 4.8 9.0 - - - +
160B VAL* 4.9 2.2 - - + -
239B VAL* 3.5 40.6 - - + -
264B ILE* 3.2 40.2 - - + -
288B TYR* 6.0 0.9 - - - -
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Residues in contact with MET 106 (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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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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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