Contacts of the strand formed by residues 441 - 446 (chain D) in PDB entry 5HP2
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 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315D LEU* 3.0 45.3 + - + +
317D LEU* 3.7 27.7 + - + +
318D HIS* 4.2 3.5 + - - -
357D MET* 3.5 6.6 - - - +
358D THR* 2.9 43.1 + - - +
439D ASN 3.6 7.1 + - - +
440D VAL* 1.3 79.0 - - - +
442D PHE* 1.3 65.0 + - - +
443D HIS* 3.7 18.0 + - - +
543D SER* 3.1 32.4 + - - +
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Residues in contact with PHE 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D VAL* 3.9 10.5 - - + -
356D VAL 3.4 1.8 - - - +
357D MET* 3.7 31.0 - - + -
369D ILE* 4.5 1.1 - - + -
403D LEU* 3.7 31.0 - - + -
406D PHE* 4.1 7.6 - + - -
407D LEU* 4.3 4.9 - - + -
425D ILE* 3.9 23.8 - - + -
436D LEU* 4.4 12.3 - - + -
440D VAL* 4.3 11.7 - - + -
441D GLN* 1.3 74.3 - - - +
443D HIS* 1.3 66.1 + - - +
528D ILE* 4.6 3.8 - - + -
540D ILE* 3.7 33.4 - - + -
541D TYR 4.7 4.4 + - - +
542D PHE* 3.5 21.4 - - + -
543D SER* 2.9 29.4 + - - +
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Residues in contact with HIS 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D HIS* 4.8 1.3 - - - -
323D LEU* 3.8 20.4 - - + +
327D VAL* 4.3 22.3 - - + +
354D GLY 3.7 0.5 - - - +
355D VAL* 3.4 4.3 - - - -
356D VAL* 2.8 51.2 + - + +
358D THR* 3.1 40.0 + - + +
441D GLN* 3.7 28.8 - - + +
442D PHE* 1.3 77.9 + - - +
444D LEU* 1.3 62.7 + - - +
445D TYR* 3.8 0.5 + - - +
542D PHE* 4.1 3.4 - - - -
543D SER* 4.2 4.5 - - - -
544D SER* 2.7 37.3 + - - -
546D ILE* 5.6 0.4 - - + -
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Residues in contact with LEU 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D GLY 3.4 19.1 - - - +
355D VAL* 4.3 3.6 - - + -
396D GLU* 4.7 8.1 - - + +
399D SER* 4.6 10.5 - - - -
443D HIS* 1.3 73.6 - - - +
445D TYR* 1.3 65.2 + - - +
446D ILE* 3.9 26.9 - - + -
520D ILE* 4.4 7.2 - - + -
523D TRP* 4.2 14.4 - - + -
542D PHE* 3.5 47.6 - - + -
544D SER 2.9 14.2 + - - +
545D ILE* 3.3 12.9 - - + +
546D ILE* 2.8 29.1 + - - +
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Residues in contact with TYR 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D VAL* 4.3 13.9 - - + -
328D SER* 3.7 39.3 + - - -
331D VAL* 4.0 35.0 - - + -
332D LEU* 5.6 3.9 - - + +
352D LEU* 4.3 15.7 - - + +
353D ALA* 3.1 6.4 - - - +
354D GLY 2.8 40.0 + - - +
356D VAL* 5.9 0.4 - - + -
443D HIS 3.8 1.0 + - - +
444D LEU* 1.3 72.4 - - - +
446D ILE* 1.3 67.3 + - - +
447D SER* 3.9 23.9 - - - -
546D ILE* 3.5 22.0 - - + -
547D LEU 4.3 1.3 - - - -
548D GLY* 3.6 32.6 - - - -
584D ILE* 4.2 4.1 - - + +
588D GLU* 4.9 7.1 + - - +
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Residues in contact with ILE 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D VAL* 4.2 10.5 - - + -
352D LEU 3.7 2.2 - - - -
353D ALA* 4.3 3.4 - - + -
396D GLU* 3.7 47.6 - - + +
444D LEU* 3.9 22.9 - - + +
445D TYR* 1.3 82.3 - - - +
447D SER* 1.3 60.0 + - - +
448D THR* 2.8 27.3 + - + +
450D PRO* 4.4 13.7 - - + -
520D ILE* 4.0 15.3 - - + -
545D ILE* 4.7 4.5 - - + -
546D ILE 2.9 10.6 + - - +
547D LEU* 3.3 12.9 - - + -
548D GLY 2.9 19.4 + - - -
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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