Contacts of the helix formed by residues 101 - 106 (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 LEU 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D PRO* 4.0 7.2 - - + +
99D TYR 2.8 16.8 + - - +
100D ASN* 1.3 75.6 - - + +
102D THR* 1.3 66.8 + - - +
103D LYS 3.3 2.1 + - - -
104D ARG* 3.6 2.4 + - - +
105D MET* 2.9 55.0 + - + +
144D VAL* 4.1 15.0 - - + -
160D VAL* 4.2 11.4 - - + -
237D PRO* 3.8 34.8 - - + -
239D VAL* 4.2 12.1 - - + +
240D MET* 4.5 4.9 - - + -
262D ARG* 4.3 8.3 - - - +
264D ILE* 3.8 19.3 - - + -
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Residues in contact with THR 102 (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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97D THR* 2.6 35.7 + - - +
98D PRO 2.8 20.3 + - - -
100D ASN 3.4 2.3 - - - -
101D LEU* 1.3 74.7 - - - +
103D LYS* 1.3 63.8 + - - +
106D MET* 2.9 32.7 + - + -
107D MET* 3.1 23.4 + - + -
124D LEU* 4.1 20.4 - - + -
126D THR* 3.8 12.3 - - + +
222E VAL* 4.8 4.7 - - + -
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Residues in contact with LYS 103 (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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100D ASN 4.3 5.7 + - - +
101D LEU 3.3 1.2 - - - -
102D THR* 1.3 79.6 - - - +
104D ARG* 1.3 98.4 + - + +
107D MET* 3.2 34.9 - - + +
108D PRO* 3.7 3.8 - - - +
221E ASN* 4.0 44.8 - - + +
222E VAL* 5.5 2.0 - - + -
224E ARG* 3.1 32.7 - - - +
225E SER* 4.9 4.8 + - - -
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Residues in contact with ARG 104 (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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100D ASN 5.2 0.8 + - - -
101D LEU 3.6 3.1 + - - +
103D LYS* 1.3 106.0 - - + +
105D MET* 1.3 63.9 + - - +
108D PRO* 3.8 15.3 - - - +
239D VAL* 3.3 28.6 - - + +
240D MET* 3.7 32.6 + - + +
243D GLU* 3.1 38.2 - - - +
244D TYR* 3.2 29.8 + - - -
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Residues in contact with MET 105 (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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98D PRO* 4.3 8.3 - - + -
101D LEU* 2.9 49.0 + - + +
104D ARG* 1.3 81.7 - - - +
106D MET* 1.3 86.9 + - + +
108D PRO* 4.4 4.5 - - - +
109D MET* 5.2 4.3 + - - +
158D GLY* 5.9 2.5 - - - -
159D SER 5.7 3.6 - - - +
160D VAL* 5.3 4.5 - - - -
239D VAL* 4.1 30.3 - - + -
264D ILE* 3.7 36.1 - - + -
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Residues in contact with MET 106 (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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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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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