Contacts of the strand formed by residues 416 - 420 (chain A) in PDB entry 1H3F
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 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A LEU* 5.5 0.7 - - + -
398A LEU* 4.0 15.7 - - + -
399A ASP* 3.2 28.4 + - - +
410A VAL* 4.1 15.5 - - + +
411A ASP* 3.0 45.4 + - - +
412A LEU* 4.0 17.3 - - + -
414A ARG* 2.8 65.1 + - - +
415A PRO* 1.3 82.2 - - - +
417A ILE* 1.3 63.3 - - - +
418A LEU* 4.0 0.4 - - + -
426A VAL 3.8 0.2 - - - +
427A ARG* 3.4 3.1 - - - -
428A VAL* 2.9 43.3 + - + +
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Residues in contact with ILE 417 (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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354A ILE* 4.4 19.5 - - + -
397A ARG 3.9 0.5 - - - +
398A LEU* 3.7 2.9 - - - +
399A ASP* 2.8 45.0 + - - +
400A GLY 4.5 2.3 + - - +
415A PRO 5.9 0.2 - - - -
416A ARG* 1.3 74.3 - - - +
418A LEU* 1.3 72.2 + - - +
419A GLN* 5.3 1.6 - - + +
425A PHE* 4.0 26.0 - - + -
426A VAL 3.6 7.0 - - - +
427A ARG* 4.2 24.9 - - + +
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Residues in contact with LEU 418 (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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374A LEU* 3.8 42.2 - - + +
375A PHE* 3.6 27.6 - - + -
378A ALA* 4.1 9.0 - - + -
380A LEU* 3.5 16.2 - - + +
397A ARG 3.6 1.6 - - - -
398A LEU* 3.4 31.6 - - + -
416A ARG* 4.9 0.7 - - + -
417A ILE* 1.3 75.0 - - - +
419A GLN* 1.3 61.0 + - - +
424A ARG 3.8 0.2 - - - +
425A PHE* 3.3 6.8 - - - +
426A VAL 2.7 38.2 + - - +
428A VAL* 4.0 26.5 - - + -
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Residues in contact with GLN 419 (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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375A PHE* 3.8 7.2 - - - -
380A LEU* 4.6 0.7 - - - -
395A GLY 3.9 0.3 - - - +
396A LEU* 3.3 5.2 - - - -
397A ARG* 2.9 68.7 + - + +
400A GLY* 5.2 5.8 - - - +
417A ILE* 5.3 2.2 - - + +
418A LEU* 1.3 76.2 - - - +
420A ARG* 1.3 64.3 + - - +
421A GLY 2.7 25.9 + - - +
422A LYS* 4.0 6.9 + - - +
424A ARG 3.1 11.9 - - - +
425A PHE* 3.0 40.4 - - + -
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Residues in contact with ARG 420 (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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380A LEU* 2.7 49.0 + - + +
381A THR* 4.1 6.5 - - - +
382A PRO* 4.4 8.3 - - - +
386A GLU* 4.2 8.7 + - - +
389A ARG* 5.1 1.8 - - - +
390A LEU* 3.6 39.3 - - + +
395A GLY 3.6 4.7 - - - +
396A LEU* 3.8 14.6 - - + -
419A GLN* 1.3 72.9 - - - +
421A GLY* 1.3 68.4 + - - +
422A LYS 3.7 0.2 + - - -
423A ASP 4.2 0.2 + - - -
424A ARG* 2.8 68.8 + - + +
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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