Contacts of the strand formed by residues 398 - 405 (chain F) in PDB entry 2W8B
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 GLY 398 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F SER* 3.4 6.7 - - - +
395F GLN 2.9 33.4 + - - +
396F GLY 3.4 1.2 + - - -
397F MET* 1.3 80.1 - - - +
399F SER* 1.3 64.4 + - - -
400F VAL* 4.2 2.2 - - - +
420F GLN* 3.4 19.1 - - - -
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Residues in contact with SER 399 (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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378F GLU* 4.8 4.9 + - - -
392F SER* 4.1 5.1 + - - -
393F SER 3.3 10.5 + - - -
394F SER* 4.4 3.8 - - - -
398F GLY* 1.3 73.3 - - - -
400F VAL* 1.3 64.2 - - - +
420F GLN* 2.9 24.0 + - - -
421F VAL 2.9 34.7 + - - -
422F LYS* 4.0 25.4 + - - +
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Residues in contact with VAL 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F SER* 3.0 21.8 - - - -
393F SER* 2.9 37.6 + - - +
395F GLN* 3.9 44.9 - - + +
398F GLY 4.2 3.1 - - - +
399F SER* 1.3 79.4 - - - +
401F LEU* 1.3 63.5 + - - +
402F ASN* 3.6 7.4 - - - +
413F ARG* 5.8 1.3 - - - -
414F LEU 5.9 0.9 - - - +
415F PRO* 6.2 4.3 - - + -
421F VAL* 3.4 14.6 - - + -
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Residues in contact with LEU 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 5.5 3.6 - - + -
167F ILE* 4.9 1.3 - - + -
169F TYR* 4.1 29.4 - - + -
390F ILE* 4.4 9.2 - - + -
391F TYR 3.4 2.7 - - - +
392F SER* 3.9 9.4 - - - -
400F VAL* 1.3 76.0 - - - +
402F ASN* 1.3 68.3 + - - +
413F ARG* 3.8 7.3 - - - +
414F LEU* 3.3 53.3 + - + +
421F VAL* 3.2 31.1 - - + +
422F LYS* 3.9 4.9 - - - +
424F PRO* 3.7 36.6 - - + -
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Residues in contact with ASN 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374F THR* 3.8 15.8 - - - +
390F ILE* 3.3 8.1 - - - +
391F TYR* 2.9 62.2 + - + +
393F SER* 2.6 43.9 + - - +
395F GLN* 5.3 0.9 - - - +
400F VAL* 3.6 7.2 - - - +
401F LEU* 1.3 80.7 + - - +
403F LEU* 1.3 62.8 + - - +
412F ALA 3.7 6.9 - - - +
413F ARG* 3.9 17.9 - - - +
414F LEU* 5.3 0.4 - - - -
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Residues in contact with LEU 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ILE* 4.0 29.2 - - + -
64F ASN 6.1 0.2 - - - +
187F TYR* 5.5 2.0 - - + +
388F MET* 4.2 13.2 - - + -
389F VAL 3.1 9.6 - - - +
390F ILE* 3.9 16.6 - - + -
391F TYR* 4.4 2.7 + - - -
402F ASN* 1.3 74.9 - - - +
404F VAL* 1.3 62.6 + - - +
410F PHE* 4.8 3.8 - - + -
411F LYS* 3.5 5.0 - - - +
412F ALA* 2.9 51.1 + - + +
413F ARG 4.7 1.3 - - - +
414F LEU* 4.0 21.5 - - + -
426F TRP* 3.6 36.8 - - + -
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Residues in contact with VAL 404 (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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358F ILE* 5.0 2.5 - - + -
371F LEU* 3.6 39.5 - - + +
372F SER* 4.8 5.2 - - - -
388F MET* 3.7 3.8 - - - -
389F VAL* 2.7 53.0 + - + +
391F TYR* 3.9 22.0 - - + +
403F LEU* 1.3 74.6 - - - +
405F SER* 1.3 71.5 + - - +
408F GLY* 4.3 6.7 - - - -
410F PHE 3.3 12.3 - - - +
411F LYS* 4.1 13.7 - - + -
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Residues in contact with SER 405 (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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65F SER 5.2 2.2 - - - -
66F GLY* 5.6 0.7 - - - -
371F LEU* 3.9 4.9 - - - +
387F THR 3.4 13.0 - - - -
388F MET* 3.7 13.6 - - - -
404F VAL* 1.3 82.4 - - - +
406F THR* 1.3 59.3 + - - +
407F ASP* 2.7 29.0 + - - -
408F GLY* 2.9 16.5 + - - -
409F ARG 3.2 1.6 + - - -
410F PHE* 3.0 39.6 + - - +
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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