Contacts of the strand formed by residues 416 - 421 (chain A) in PDB entry 1HNY
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 GLN 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A TYR* 3.9 5.1 + - - -
411A ASP* 3.3 3.8 - - - -
412A ASN* 3.1 48.0 + - + +
414A SER 3.7 0.4 - - - -
415A ASN* 1.3 77.5 - - - +
417A VAL* 1.3 63.2 - - - +
429A PHE 3.2 5.2 - - - +
430A ASN* 3.1 28.2 + - - +
432A ASP* 3.2 13.5 - - - +
434A TRP* 3.1 39.6 + - - +
435A SER 3.5 6.2 + - - +
436A PHE* 3.3 37.7 - - + +
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Residues in contact with VAL 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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274A MET* 3.4 63.7 - - + +
275A SER* 3.8 5.2 - - - +
327A PHE* 5.3 1.6 - - + -
409A TRP* 3.9 20.4 - - + -
410A TYR* 3.2 13.0 - - - +
411A ASP* 3.8 12.6 - - + -
415A ASN 3.8 0.6 - - - -
416A GLN* 1.3 83.4 - - - +
418A ALA* 1.3 61.0 + - - +
419A PHE* 5.3 2.0 - - + -
428A VAL* 3.6 2.1 - - - +
429A PHE* 2.7 46.0 + - + +
436A PHE* 6.0 0.7 - - - -
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Residues in contact with ALA 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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408A ASN 4.2 1.1 - - - -
409A TRP* 3.3 3.3 - - - -
410A TYR* 2.8 36.8 + - + +
417A VAL* 1.3 76.8 - - - +
419A PHE* 1.3 70.7 + - - +
426A PHE* 3.7 20.9 - - + -
427A ILE 3.1 15.3 - - - +
428A VAL* 4.0 5.8 - - + -
429A PHE* 5.2 0.7 - - - -
436A PHE* 5.7 0.2 - - + -
440A LEU* 3.7 21.3 - - + -
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Residues in contact with PHE 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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327A PHE* 3.6 32.8 - + - -
330A ALA* 3.6 46.2 - - + -
331A HIS* 4.0 8.1 - - + -
406A PHE* 3.5 35.9 - + + -
407A THR 3.7 8.1 - - - +
408A ASN 3.8 5.8 - - - -
409A TRP* 3.9 18.2 - + + -
417A VAL* 5.3 0.7 - - + -
418A ALA* 1.3 79.6 - - - +
420A GLY* 1.3 69.9 + - - +
421A ARG* 4.3 6.1 - - + -
426A PHE* 3.4 8.0 - - - -
427A ILE* 3.0 45.9 + - + +
429A PHE* 4.2 6.1 - + - -
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Residues in contact with GLY 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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397A PHE* 6.3 0.2 - - - -
406A PHE* 3.7 0.5 - - - -
407A THR* 2.7 40.3 + - - +
408A ASN* 4.8 1.3 - - - -
419A PHE* 1.3 84.8 - - - +
421A ARG* 1.3 67.7 + - - -
422A GLY 5.1 1.1 - - - -
425A GLY 3.2 13.0 - - - -
426A PHE* 3.6 12.7 - - - -
442A THR 4.8 2.5 - - - -
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Residues in contact with ARG 421 (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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329A LEU 4.7 0.4 + - - -
330A ALA 2.8 40.3 + - - +
331A HIS 3.9 0.8 + - - -
332A PRO* 3.6 41.8 - - - +
397A PHE* 4.3 9.9 - - + -
398A ARG* 4.5 7.9 + - - +
401A VAL* 3.5 54.5 + - + +
402A ASP* 4.6 2.4 - - - +
403A GLY 4.2 6.1 - - - +
404A GLN* 2.7 40.2 + - + +
405A PRO 3.3 6.8 - - - -
406A PHE* 4.5 2.5 - - - +
419A PHE* 4.3 7.6 - - + -
420A GLY* 1.3 79.4 - - - -
422A GLY* 1.3 66.7 + - - +
424A ARG* 3.0 16.8 + - - +
425A GLY 2.9 11.6 + - - +
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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