Contacts of the helix formed by residues 201 - 206 (chain A) in PDB entry 3U44
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.9 23.8 - - + -
197A TRP* 3.3 58.6 - + - -
198A LEU* 3.0 14.3 + - + +
200A SER* 1.3 79.2 - - - +
202A VAL* 1.3 62.7 + - - +
203A HIS 3.3 0.7 + - - -
204A LEU* 3.3 20.1 + - - +
205A TYR* 3.6 9.4 - - - -
342A ILE* 4.0 11.0 - - + -
345A LEU* 5.6 3.8 - - + -
346A VAL* 3.5 25.4 - - + -
824A LEU* 4.1 8.3 - - + -
828A LEU 5.9 1.1 - - - -
829A GLY* 3.9 5.6 - - - -
830A PHE* 3.5 51.5 - + + +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.3 19.5 - - - +
201A PHE* 1.3 72.7 - - + +
203A HIS* 1.3 77.0 + - + +
204A LEU 3.0 2.9 - - - -
205A TYR* 2.8 24.2 + - - +
206A ASP* 3.1 13.3 + - - +
339A LYS* 4.9 11.9 - - + +
342A ILE* 4.4 10.1 - - + -
343A GLU* 3.5 43.3 - - + +
346A VAL* 5.0 6.3 - - + -
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Residues in contact with HIS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.8 16.2 + - + +
200A SER* 3.6 26.3 - - - +
201A PHE 3.2 0.8 - - - -
202A VAL* 1.3 86.6 - - + +
204A LEU* 1.3 61.0 + - - +
206A ASP* 3.8 18.6 + - - +
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A SER 4.2 2.8 + - - +
201A PHE 3.3 11.3 + - - +
202A VAL 3.0 1.0 - - - -
203A HIS* 1.3 81.3 - - - +
205A TYR* 1.3 70.1 + - + +
206A ASP 3.2 6.1 + - - +
207A VAL* 4.7 3.8 - - - +
216A LEU* 5.6 5.4 - - + +
217A PRO* 5.7 8.1 - - + -
218A PHE* 3.6 36.1 - - + -
335A LEU* 4.5 8.2 - - + +
828A LEU* 3.9 26.2 - - + +
830A PHE 3.5 24.5 - - - +
847A PRO* 4.1 21.8 - - + -
851A MET* 5.8 0.7 - - - -
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE 3.6 16.2 - - - -
202A VAL* 2.8 9.1 + - - +
204A LEU* 1.3 87.2 - - + +
206A ASP* 1.3 58.8 + - - +
207A VAL* 3.4 7.7 + - - +
335A LEU* 3.3 44.2 - - + -
336A ALA* 3.6 20.1 - - - +
338A MET* 4.1 10.3 - - + -
339A LYS* 3.7 26.6 - - + +
342A ILE* 3.8 37.5 - - + -
830A PHE* 3.2 18.0 + - + -
831A GLY* 3.2 27.5 - - - -
832A THR* 3.3 17.8 + - + +
845A THR* 5.3 1.9 - - + +
847A PRO* 5.3 2.3 - - + +
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Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL 3.1 11.7 + - - +
203A HIS* 4.0 15.9 - - - +
204A LEU 3.2 2.2 - - - +
205A TYR* 1.3 74.7 - - - +
207A VAL* 1.3 63.3 + - - +
339A LYS* 3.5 31.3 + - - +
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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