Contacts of the helix formed by residues 101 - 106 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E PRO* 4.1 9.4 - - + +
99E TYR 3.0 9.3 + - - +
100E ASN* 1.3 81.6 - - + +
102E THR* 1.3 64.3 + - - +
103E LYS 3.2 0.6 + - - -
104E ARG* 3.6 2.5 + - - +
105E MET* 3.0 46.0 + - + +
144E VAL* 3.8 29.4 - - + -
160E VAL* 4.3 9.9 - - + -
237E PRO* 3.9 32.1 - - + -
239E VAL* 4.2 12.9 - - + +
240E MET* 4.3 4.7 - - + -
262E ARG* 4.4 8.5 - - - +
264E ILE* 4.0 15.5 - - + -
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Residues in contact with THR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ASN* 6.1 0.4 - - - -
222D VAL* 4.0 16.2 - - + -
97E THR* 2.7 34.5 + - - +
98E PRO* 2.6 23.8 + - - -
100E ASN 3.3 2.9 - - - -
101E LEU* 1.3 77.0 - - - +
103E LYS* 1.3 64.7 + - - +
106E MET* 2.9 33.9 + - + -
107E MET* 3.0 13.9 + - - -
124E LEU* 4.0 18.2 - - + -
126E THR* 3.7 11.0 - - + +
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Residues in contact with LYS 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ASN* 3.9 46.0 - - + +
222D VAL* 4.8 2.0 - - + +
224D ARG* 4.0 27.9 - - - +
225D SER* 4.6 10.9 + - - -
244D TYR* 5.7 2.0 + - - -
100E ASN 4.3 6.5 + - - +
101E LEU 3.3 0.6 - - - -
102E THR* 1.3 78.9 - - - +
104E ARG* 1.3 96.8 + - + +
107E MET* 3.2 29.7 - - + +
108E PRO* 3.7 4.0 - - - +
244E TYR* 5.8 0.6 + - - -
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Residues in contact with ARG 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ARG* 5.9 0.4 - - - +
100E ASN 5.2 0.8 + - - +
101E LEU 3.6 3.3 + - - +
103E LYS* 1.3 114.3 - - + +
105E MET* 1.3 64.1 + - - +
108E PRO* 3.8 16.1 - - - +
239E VAL* 3.3 33.2 - - + +
240E MET* 4.0 23.6 + - + +
243E GLU* 2.8 37.8 + - - +
244E TYR* 4.4 11.5 + - - -
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Residues in contact with MET 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E PRO* 4.7 5.4 - - + -
101E LEU* 3.0 35.4 + - + +
104E ARG* 1.3 80.8 - - - +
106E MET* 1.3 75.7 + - + +
108E PRO* 4.4 3.9 - - - +
109E MET* 5.2 5.0 + - - +
157E ILE* 6.3 0.4 - - + -
158E GLY* 5.9 2.0 - - - -
159E SER 5.5 2.9 - - - +
160E VAL* 3.9 24.0 - - - -
239E VAL* 3.9 17.3 - - + -
264E ILE* 3.5 44.6 - - + -
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Residues in contact with MET 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E THR* 4.5 9.6 - - + -
98E PRO* 4.8 2.0 - - + -
102E THR* 2.9 33.4 + - + +
105E MET* 1.3 102.9 - - + +
107E MET* 1.3 66.4 + - - +
108E PRO* 3.4 2.5 - - - -
109E MET* 3.2 27.9 + - + +
110E LEU* 2.9 32.6 + - + +
142E PHE* 3.5 55.6 - - + -
157E ILE* 4.6 10.3 - - + -
264E ILE* 4.9 0.4 - - - -
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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