Contacts of the strand formed by residues 369 - 375 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C LYS* 3.5 14.8 + - - +
212C GLU 5.3 3.4 - - - -
431C SO4 2.5 63.8 + - - +
359E PHE* 3.9 26.3 - - + -
360E ALA* 4.0 0.2 - - - -
361E ASP* 3.0 34.6 + - + +
367E ARG* 3.5 3.1 - - - +
368E GLU* 1.3 103.9 + - - +
370E VAL* 1.3 71.2 + - - +
371E ILE* 5.3 7.0 - - + -
411E LEU 4.3 9.9 + - - -
412E LYS* 3.5 36.6 + - - +
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Residues in contact with VAL 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ALA 4.4 1.8 - - - +
212C GLU* 3.6 28.2 + - + +
214C ASN* 5.8 2.9 - - + -
199E ILE* 4.0 16.8 - - + -
200E GLY* 3.7 25.1 - - - +
359E PHE* 3.1 13.7 - - - +
360E ALA* 4.1 1.1 - - - -
367E ARG* 3.6 33.9 - - + +
369E ARG* 1.3 83.1 - - - +
371E ILE* 1.3 71.2 + - - +
372E THR* 5.0 2.7 - - + +
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Residues in contact with ILE 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E PHE* 3.5 10.6 - - + +
358E PHE* 3.4 4.3 - - - -
359E PHE* 2.8 55.0 + - + +
369E ARG* 5.3 7.2 - - + -
370E VAL* 1.3 80.1 - - - +
372E THR* 1.3 66.0 + - - +
373E LYS* 3.7 34.8 - - + -
410E PHE 5.7 0.4 - - - +
411E LEU* 3.7 29.8 - - + -
600E LMT 4.0 16.2 - - + -
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Residues in contact with THR 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C GLU* 5.7 4.0 + - - +
199E ILE* 3.0 37.5 - - + +
200E GLY* 4.1 6.7 - - - -
201E ALA* 4.3 14.0 + - - +
202E SER 4.7 1.1 - - - +
205E LEU* 4.5 13.7 - - - +
357E PHE 3.3 4.5 - - - -
358E PHE* 3.8 21.3 - - + -
370E VAL* 5.0 2.1 - - + +
371E ILE* 1.3 79.2 - - - +
373E LYS* 1.3 64.6 + - - +
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Residues in contact with LYS 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E LEU* 4.7 8.0 - - - +
356E GLY* 3.5 3.1 - - - -
357E PHE* 2.6 43.4 + - + +
358E PHE* 5.7 0.2 - - - -
371E ILE* 3.7 24.7 - - + -
372E THR* 1.3 79.3 - - - +
374E MET* 1.3 59.8 + - - +
377E TRP* 4.0 17.7 - - + +
600E LMT 2.6 67.9 + - - +
600F LMT 5.2 2.4 + - - -
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Residues in contact with MET 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E LEU* 4.9 16.4 - - + -
209E LEU* 3.6 33.2 - - + -
212E GLU* 5.6 2.7 - - - +
213E ARG* 5.1 2.7 - - - +
351E PHE* 4.1 10.8 - - + -
354E ASP* 4.2 16.2 - - - +
355E ALA 3.3 25.4 - - - +
356E GLY* 4.0 5.8 - - - +
357E PHE* 5.5 0.4 - - - -
373E LYS* 1.3 77.6 - - - +
375E GLY* 1.3 59.8 + - - +
377E TRP* 4.2 9.3 + - - -
434E SO4 4.8 2.3 + - - -
600E LMT 5.3 2.9 + - - -
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Residues in contact with GLY 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E ASP* 3.6 9.0 - - - -
355E ALA 3.0 27.1 + - - +
374E MET* 1.3 79.4 - - - +
376E LYS* 1.3 66.2 + - - -
377E TRP* 3.3 11.9 - - - +
378E ALA* 3.4 8.8 + - - +
434E SO4 3.5 11.2 - - - -
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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