Contacts of the strand formed by residues 357 - 361 (chain A) in PDB entry 4KM5
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 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 3.8 30.1 - - + -
326A SER* 3.0 66.6 + - - +
328A SER* 3.5 14.4 - - - -
329A SER 3.3 23.3 - - - -
330A TRP* 3.7 16.4 - + + +
331A PRO* 4.1 8.3 - - + -
356A PRO* 1.3 72.2 - - - +
358A TYR* 1.3 73.5 + - - +
359A LEU* 4.6 7.4 - - + -
377A LEU* 3.7 23.8 - - + -
379A PHE* 3.6 27.1 - - + -
381A HIS* 4.3 3.6 - - - -
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.2 40.2 - - + +
229A MET* 5.5 1.1 - - - -
231A LYS* 3.9 21.1 - - + +
323A ALA* 4.5 11.7 - - + -
324A LEU 3.2 17.3 - - - +
325A GLU* 2.9 44.7 + - + -
356A PRO* 3.6 24.6 - - + +
357A PHE* 1.3 78.2 - - - +
359A LEU* 1.3 62.2 - - - +
377A LEU* 3.4 6.2 - - - +
378A SER* 2.6 49.3 + - - +
381A HIS* 3.5 26.5 - + - -
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Residues in contact with LEU 359 (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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237A ILE* 5.2 4.7 - - + -
239A LEU* 3.7 30.7 - - + -
249A TYR* 4.8 8.7 - - + -
251A VAL* 3.8 16.8 - - + -
323A ALA* 3.3 5.9 - - - -
324A LEU* 2.9 49.7 + - + +
326A SER* 5.8 4.5 - - - -
357A PHE* 4.6 7.0 - - + -
358A TYR* 1.3 75.5 - - - +
360A VAL* 1.3 62.0 + - - +
375A TRP* 3.8 32.7 - - + +
376A ARG 3.3 9.2 - - - +
377A LEU* 3.6 28.5 - - + -
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A MET* 4.8 6.1 - - + -
306A PRO* 4.4 4.5 - - + -
321A THR* 3.8 22.9 - - + -
323A ALA* 4.0 15.9 - - + -
359A LEU* 1.3 78.7 - - - +
361A PRO* 1.3 84.1 - - + +
375A TRP* 3.9 2.7 - - - -
376A ARG* 2.6 65.2 + - - +
378A SER* 3.7 26.5 - - - +
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Residues in contact with PRO 361 (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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273A ALA* 3.8 24.2 - - + -
277A LEU* 4.0 20.0 - - + -
306A PRO* 3.4 28.8 - - + +
322A LEU* 3.3 22.7 - - + +
359A LEU 4.1 0.2 - - - +
360A VAL* 1.3 102.3 - - + +
362A LYS* 1.3 67.9 + - - +
363A HIS* 5.7 0.2 + - - -
374A THR 4.3 6.1 - - - +
375A TRP* 3.5 22.2 - - + -
376A ARG* 5.5 1.4 + - - +
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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