Contacts of the helix formed by residues 288 - 292 (chain M) in PDB entry 4HOK
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 PHE 288 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M THR* 3.5 16.8 - - + +
107M LEU* 3.5 34.1 - - + -
108M LEU* 4.0 15.7 - - + -
111M GLN* 4.6 4.0 - - - -
136M MET* 3.6 26.0 - - + -
142M GLY 4.1 2.9 - - - -
143M ASN* 4.1 16.8 - - - -
286M TYR* 3.1 34.7 + + + -
287M VAL* 1.3 80.1 - - - +
289M ASP* 1.3 68.9 + - - +
290M TRP* 3.2 37.2 - + + -
291M ASN* 3.0 33.0 + - - +
292M MET* 3.8 3.5 + - - +
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Residues in contact with ASP 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96M CYS* 3.8 19.3 - - + -
99M LYS 4.9 2.0 - - - -
100M PHE* 3.5 9.9 - - + +
101M SER* 2.9 44.6 + - - -
104M THR* 2.7 31.8 + - - +
288M PHE* 1.3 72.7 - - - +
290M TRP* 1.3 63.4 + - + +
292M MET* 3.2 32.4 + - - +
294M LYS* 3.6 13.3 + - - +
13O ARG* 3.7 11.3 + - - -
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Residues in contact with TRP 290 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M LEU* 4.4 4.0 - - + -
92M LEU* 3.7 42.7 - - + +
95M PHE* 3.6 27.8 - - + -
96M CYS* 3.7 10.5 - - - -
100M PHE* 3.7 25.6 - + - -
104M THR* 3.7 20.2 - - + -
108M LEU* 4.0 17.5 - - + -
136M MET* 3.8 25.1 - - + +
142M GLY 4.9 4.0 + - - -
288M PHE* 3.4 39.0 - + + -
289M ASP* 1.3 76.7 - - - +
291M ASN* 1.3 84.8 + - - +
292M MET 3.2 1.5 + - - -
294M LYS* 4.5 1.1 - - - +
87O PRO* 3.6 18.0 - - - +
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Residues in contact with ASN 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M GLY 5.6 3.0 + - - -
286M TYR 3.6 5.5 - - - +
287M VAL* 4.4 10.1 - - + -
288M PHE* 3.0 49.1 + - - +
290M TRP* 1.3 90.9 + - - +
292M MET* 1.3 58.2 + - - +
85O LEU 4.1 0.2 - - - +
86O GLY* 3.1 23.6 - - - -
87O PRO* 3.2 5.0 - - - +
137O GLY 5.0 1.2 - - - +
138O LEU* 4.2 15.3 - - + +
139O GLY* 5.8 2.2 - - - +
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Residues in contact with MET 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M LYS* 5.7 1.6 - - + +
287M VAL* 3.4 37.0 - - + +
288M PHE 4.2 7.0 - - - +
289M ASP* 3.2 20.8 + - - +
290M TRP 3.2 1.1 - - - +
291M ASN* 1.3 79.9 - - - +
293M LEU* 1.3 72.9 + - - +
294M LYS* 3.1 13.7 - - - +
13O ARG* 5.2 5.4 - - - +
15O ILE* 3.7 26.5 - - + -
25O LEU* 4.0 16.8 - - + -
34O GLU* 3.7 16.6 - - - +
84O LEU* 3.8 22.0 - - + -
85O LEU 3.8 5.6 - - - -
87O PRO* 3.2 13.8 - - - +
138O LEU* 4.7 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