Contacts of the strand formed by residues 369 - 375 (chain F) in PDB entry 3HYW
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 ARG 369 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B LYS* 4.0 12.6 - - - +
212B GLU 5.9 0.2 - - - -
342F ARG* 5.8 0.2 - - - +
359F PHE* 4.7 11.1 - - + -
360F ALA* 3.9 0.2 - - - -
361F ASP* 2.9 47.3 + - + +
367F ARG* 3.4 3.4 - - - +
368F GLU* 1.3 96.8 - - + +
370F VAL* 1.3 73.6 + - - +
371F ILE* 5.5 7.2 - - + -
411F LEU* 4.1 10.0 + - - +
412F LYS* 3.6 39.3 + - - +
431F SO4 2.5 57.7 + - - +
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Residues in contact with VAL 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ALA 4.6 0.7 - - - +
212B GLU* 3.3 30.6 + - + +
214B ASN* 5.9 2.9 - - + +
199F ILE* 3.9 18.2 - - + -
200F GLY* 3.7 26.2 - - - +
359F PHE* 3.0 14.6 - - - +
360F ALA* 4.1 0.7 - - - -
367F ARG* 3.5 29.2 - - + +
369F ARG* 1.3 83.8 - - - +
371F ILE* 1.3 70.6 + - - +
372F THR* 5.0 1.8 - - + -
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Residues in contact with ILE 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F PHE* 3.5 14.5 - - + +
358F PHE* 3.4 5.2 - - - -
359F PHE* 2.8 53.2 + - + +
369F ARG* 5.5 8.7 - - + -
370F VAL* 1.3 78.4 - - - +
372F THR* 1.3 67.0 + - - +
373F LYS* 3.8 37.2 - - + +
410F PHE 5.8 0.2 - - - +
411F LEU* 3.6 30.7 - - + -
600F LMT 5.5 7.4 - - + -
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Residues in contact with THR 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLU* 5.5 4.5 - - - +
199F ILE* 2.9 42.2 - - + +
200F GLY* 3.9 7.3 - - - -
201F ALA* 4.3 12.8 + - - +
202F SER 4.7 1.1 - - - +
205F LEU* 4.3 19.7 - - - +
357F PHE 3.4 4.0 - - - -
358F PHE* 4.0 9.6 - - + -
370F VAL* 5.0 1.3 - - + +
371F ILE* 1.3 80.7 - - - +
373F LYS* 1.3 66.8 + - - +
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Residues in contact with LYS 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600E LMT 5.2 2.4 - - - -
205F LEU* 4.6 8.8 - - - +
356F GLY* 3.4 3.8 - - - -
357F PHE* 2.7 42.7 + - + +
358F PHE* 5.6 0.2 - - - -
371F ILE* 3.8 24.1 - - + +
372F THR* 1.3 79.7 - - - +
374F MET* 1.3 60.3 + - - +
377F TRP* 3.8 16.8 - - + +
600F LMT 2.9 67.8 + - - +
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Residues in contact with MET 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F LEU* 4.4 18.4 - - + +
209F LEU* 3.6 40.8 - - + -
212F GLU* 5.3 4.9 - - - +
213F ARG* 4.8 7.9 - - - +
351F PHE* 4.3 7.0 - - + -
354F ASP* 5.0 5.6 - - - +
355F ALA 3.4 19.7 - - - +
356F GLY* 4.5 1.1 - - - -
373F LYS* 1.3 76.4 - - - +
375F GLY* 1.3 62.1 + - - +
377F TRP* 4.1 9.8 + - - -
378F ALA* 5.6 0.2 - - - -
434F SO4 4.3 1.4 + - - -
600F LMT 4.2 10.6 + - - -
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Residues in contact with GLY 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F ASP* 3.8 9.0 - - - -
355F ALA 3.1 26.6 + - - +
374F MET* 1.3 78.4 - - - +
376F LYS* 1.3 66.9 + - - -
377F TRP* 3.2 9.4 - - - +
378F ALA* 3.4 8.1 + - - +
434F SO4 3.4 17.5 - - - -
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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