Contacts of the strand formed by residues 198 - 203 (chain B) in PDB entry 3IXK
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 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B THR* 4.0 12.1 - - + -
169B LEU* 3.7 34.8 - - + -
185B PHE* 3.9 29.6 - + + -
197B LEU* 1.3 75.2 - - - +
199B SER* 1.3 61.5 + - - +
200B LEU* 4.2 11.9 - - + -
222B MET* 4.9 9.4 - - + -
223B ILE 3.2 13.9 - - - +
224B ILE* 4.4 3.6 - - - -
225B GLY 4.3 0.2 - - - +
226B GLY 4.5 1.6 - - - -
247B TYR* 3.3 26.2 - + - -
392B VAL* 3.6 3.8 - - - +
393B PHE* 2.6 78.9 + + + +
395B ARG* 4.0 9.0 - - - -
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Residues in contact with SER 199 (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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198B PHE* 1.3 77.7 - - - +
200B LEU* 1.3 64.6 + - - +
221B SER 3.7 0.5 - - - +
222B MET* 3.2 6.2 - - - +
223B ILE* 2.8 33.9 + - - +
226B GLY 2.9 17.8 + - - -
227B ILE* 5.0 0.4 - - - -
390B TYR* 2.8 35.1 + - - -
391B VAL 3.3 12.8 - - - -
392B VAL* 4.0 12.6 - - - -
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 4.2 9.6 - - + -
79B VAL* 3.8 25.1 - - + -
81B THR* 3.9 28.0 - - + -
198B PHE* 4.2 7.4 - - + -
199B SER* 1.3 73.9 - - - +
201B GLN* 1.3 61.6 + - - +
202B LEU* 3.9 10.6 + - + +
221B SER 3.4 2.7 - - - +
222B MET* 3.5 35.4 - - + -
277B SER* 4.0 6.5 - - - -
386B MET* 4.0 20.7 - - + +
389B PHE 3.9 2.4 - - - +
390B TYR* 3.7 3.4 - - - -
391B VAL* 2.9 33.5 + - - +
393B PHE* 3.9 14.4 - - + -
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Residues in contact with GLN 201 (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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52B ASP* 4.9 3.8 - - - +
199B SER 4.2 0.2 - - - -
200B LEU* 1.3 72.8 - - - +
202B LEU* 1.3 62.7 + - - +
203B CYS* 3.9 5.1 - - - -
220B GLY* 2.9 8.3 - - - -
221B SER* 2.8 58.4 + - - +
231B LEU* 3.3 37.0 + - + +
389B PHE 4.2 3.4 - - - -
390B TYR* 3.7 19.7 - - + -
405B SER* 3.0 29.9 + - - +
406B ALA* 3.8 9.7 - - - +
407B CYS* 3.7 21.4 - - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.6 22.9 - - + -
62B TYR* 3.5 48.0 - - + -
79B VAL* 6.1 0.9 - - + -
200B LEU* 3.9 16.5 + - + +
201B GLN* 1.3 73.5 - - - +
203B CYS* 1.3 62.9 + - - +
219B GLY 4.2 1.6 - - - -
277B SER* 4.3 22.2 - - - +
383B ALA* 4.6 9.6 - - + -
386B MET* 4.0 26.7 + - + +
387B GLU* 3.0 39.9 - - + +
389B PHE 4.4 4.4 + - - -
407B CYS* 4.2 0.5 - - - -
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Residues in contact with CYS 203 (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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52B ASP* 6.0 0.9 - - - -
62B TYR* 3.2 11.7 + - - -
201B GLN* 3.9 15.3 - - - -
202B LEU* 1.3 73.0 - - - +
204B GLY* 1.3 67.4 + - - +
218B VAL* 3.8 2.8 - - - +
219B GLY* 3.0 33.7 + - - +
220B GLY* 4.2 9.6 - - - -
407B CYS* 2.0 51.4 - - + +
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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
------------------------------------------------------------
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