Contacts of the strand formed by residues 388 - 392 (chain D) in PDB entry 5HP1
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 LYS 388 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ASP* 5.8 3.8 - - + -
325D LEU 2.6 15.6 + - - +
326D ILE* 3.3 20.1 - - + +
327D ALA 2.8 24.5 + - - +
386D THR 4.0 0.2 + - - -
387D PRO* 1.3 73.0 - - - +
389D PHE* 1.3 69.3 + - - +
390D LYS* 6.0 0.9 - - + -
413D GLU* 3.6 35.4 - - + +
414D TRP* 4.7 2.7 - - - -
415D GLU* 3.2 32.9 + - - +
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Residues in contact with PHE 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ALA* 3.3 24.7 - - + -
329D ILE* 4.0 17.0 - - + -
372D VAL* 3.5 28.0 - - + -
375D ILE* 3.8 22.4 - - + -
376D THR* 3.1 28.7 - - - -
387D PRO* 3.5 33.2 - - + -
388D LYS* 1.3 74.7 - - - +
390D LYS* 1.3 58.0 + - - +
391D LEU* 3.6 19.7 - - + -
412D PRO* 3.7 13.5 - - + -
413D GLU 3.1 17.4 + - - +
414D TRP* 4.1 2.9 - - + -
415D GLU* 2.7 35.9 + - - +
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Residues in contact with LYS 390 (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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326D ILE* 4.2 17.7 - - + +
327D ALA 2.7 15.8 + - - +
328D GLU* 3.7 29.5 + - + +
329D ILE* 3.7 16.6 + - - +
342D TYR* 3.6 17.1 + - - +
388D LYS* 6.0 1.3 - - + -
389D PHE* 1.3 71.5 - - - +
391D LEU* 1.3 63.5 + - - +
392D PRO* 3.6 7.6 - - - +
415D GLU* 3.1 34.5 - - + +
417D VAL* 3.9 27.4 - - + +
15E C 4.5 15.1 + - - -
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Residues in contact with LEU 391 (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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329D ILE* 4.4 7.2 - - + -
368D LEU* 4.6 4.7 - - + -
372D VAL* 3.7 24.7 - - + -
389D PHE* 3.6 27.8 - - + -
390D LYS* 1.3 73.1 - - - +
392D PRO* 1.3 66.2 - - + +
393D ILE* 2.9 21.8 + - + +
398D TRP* 3.8 34.1 - - + -
414D TRP* 3.7 23.6 - - + -
415D GLU 2.7 17.1 + - - +
416D PHE* 3.6 15.2 - - + -
417D VAL* 3.0 22.2 + - - +
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Residues in contact with PRO 392 (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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406C TRP* 4.4 13.5 - - + +
407C GLN* 3.5 8.4 - - + +
408C ALA* 2.9 24.9 + - - +
329D ILE* 3.1 47.1 - - + +
330D GLN* 4.9 0.9 - - - -
331D LYS 4.6 5.6 - - - +
337D TRP* 4.4 14.4 - - + -
368D LEU* 4.4 8.3 - - + -
390D LYS 3.6 4.5 - - - +
391D LEU* 1.3 80.0 - - + +
393D ILE* 1.3 61.0 + - - +
417D VAL* 3.8 13.2 - - + +
419D THR 6.3 0.7 - - - +
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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