Contacts of the strand formed by residues 395 - 406 (chain A) in PDB entry 1HPL
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 LEU 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A TYR* 4.7 1.3 - - + -
359A LEU* 4.2 13.7 - - + -
360A PHE 3.8 5.2 - - - +
361A GLY* 3.9 1.6 - - - -
392A VAL* 4.0 16.2 - - + -
393A GLY 3.9 11.2 - - - +
394A ASP* 1.3 74.6 - - - +
396A GLU* 1.3 60.2 + - - +
397A LYS 4.6 2.5 - - - +
398A VAL* 4.1 15.5 - - + -
422A VAL* 3.7 39.0 - - + -
424A ARG* 4.3 12.8 - - + -
430A PHE* 3.8 43.7 - - + -
432A PHE* 3.9 16.6 - - + -
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Residues in contact with GLU 396 (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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360A PHE* 2.9 15.6 + - - +
361A GLY* 3.9 14.0 - - - -
362A ASN* 4.0 17.5 + - - +
394A ASP 4.7 1.1 - - - +
395A LEU* 1.3 74.4 - - - +
397A LYS* 1.4 93.7 + - + +
432A PHE* 3.4 14.1 - - - -
447A THR* 5.2 0.9 - - - +
448A ALA* 4.7 8.0 + - - +
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Residues in contact with LYS 397 (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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360A PHE* 2.9 62.0 + - + +
395A LEU* 4.6 1.7 - - - +
396A GLU* 1.4 104.4 + - - +
398A VAL* 1.3 70.2 + - - +
399A LYS* 4.7 8.1 - - - +
432A PHE* 3.6 10.9 - - - -
445A THR* 3.9 22.9 - - + -
446A LEU 3.5 12.3 - - - +
447A THR* 5.2 4.7 - - + -
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Residues in contact with VAL 398 (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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357A VAL* 3.7 23.3 - - + -
358A SER 3.4 5.2 - - - +
359A LEU* 3.9 14.6 - - + -
360A PHE* 4.7 0.4 - - - -
395A LEU* 4.1 5.2 - - + -
397A LYS* 1.3 79.4 - - - +
399A LYS* 1.3 67.5 + - - +
420A ILE* 3.8 29.6 - - + -
422A VAL* 3.8 26.9 - - + -
432A PHE* 4.0 17.7 - - + -
445A THR* 3.6 2.9 - - - +
446A LEU* 2.8 32.0 + - + +
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Residues in contact with LYS 399 (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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357A VAL* 3.2 8.8 - - - +
358A SER* 2.9 44.9 + - - +
360A PHE* 3.4 42.7 - - + -
397A LYS* 4.7 11.5 - - + +
398A VAL* 1.3 80.4 - - - +
400A PHE* 1.3 59.9 + - - +
443A LEU* 3.7 35.4 - - + -
444A LEU 3.2 7.2 - - - +
445A THR* 3.7 25.2 + - - +
446A LEU* 4.7 0.4 - - - -
47B ASP* 4.6 14.9 + - - -
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Residues in contact with PHE 400 (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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344A VAL* 4.2 5.2 - - + -
346A LEU* 3.8 24.5 - - + -
355A VAL* 3.7 35.7 - - + -
356A LEU 3.6 11.0 - - - -
357A VAL* 4.4 1.6 - - + -
399A LYS* 1.3 75.4 - - - +
401A ILE* 1.3 66.3 + - - +
402A TRP* 3.9 24.7 - + + -
415A VAL* 4.0 18.6 - - + -
416A GLY* 4.0 9.9 - - - -
417A ALA* 4.0 13.7 - - + -
420A ILE* 4.2 8.7 - - + -
438A VAL* 4.7 2.7 - - + -
442A VAL 3.6 0.5 - - - +
443A LEU* 3.5 4.7 - - - +
444A LEU* 2.9 51.9 + - + +
446A LEU* 4.1 13.9 - - + -
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Residues in contact with ILE 401 (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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355A VAL* 3.7 1.6 - - - -
356A LEU* 3.0 56.2 + - + +
368A GLN* 4.0 19.7 - - - +
400A PHE* 1.3 82.9 - - - +
402A TRP* 1.3 66.0 + - - +
403A TYR* 3.6 23.1 - - + +
441A ASP* 3.7 27.4 - - - +
442A VAL 3.7 23.3 - - - +
443A LEU* 3.9 15.7 - - + +
48B ASN* 5.7 0.2 - - - +
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Residues in contact with TRP 402 (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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351A VAL* 3.4 43.7 - - + -
354A HIS 3.2 12.3 - - - +
355A VAL* 3.9 16.6 - - + -
376A LEU* 4.6 3.4 - - + -
400A PHE* 3.9 12.3 - + + -
401A ILE* 1.3 75.6 - - - +
403A TYR* 1.3 82.9 + - - +
404A ASN* 3.6 22.2 - - + -
413A PRO* 3.4 27.8 - - + -
415A VAL* 3.4 30.0 + - + -
438A VAL* 2.8 25.2 + - + -
439A ARG 3.4 9.9 + - - -
440A GLU* 3.3 26.8 - - + -
441A ASP* 3.0 24.9 + - - -
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Residues in contact with TYR 403 (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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353A GLY* 3.0 24.6 - - - -
354A HIS* 3.0 44.5 + - + +
356A LEU* 3.6 23.3 - - + -
368A GLN* 5.1 3.4 + - - -
401A ILE* 3.6 28.8 - - + +
402A TRP* 1.3 79.3 - - - +
404A ASN* 1.3 61.9 + - - +
406A ASN 3.9 0.2 + - - -
440A GLU* 3.7 11.2 - - - +
441A ASP* 3.1 37.0 + - + -
83B GLU* 3.9 33.7 - - + -
84B SER* 3.9 21.0 - - - -
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Residues in contact with ASN 404 (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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351A VAL* 4.4 3.8 - - - +
352A THR* 2.8 35.5 + - - +
402A TRP* 3.6 20.8 - - + -
403A TYR* 1.3 75.0 - - - +
406A ASN* 1.3 64.7 + - - +
407A VAL* 3.3 42.3 + - - +
409A ASN* 3.9 13.7 + - - +
413A PRO* 4.3 15.1 - - - +
440A GLU* 2.9 24.8 + - + +
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Residues in contact with ASN 406 (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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352A THR* 3.1 28.6 + - - +
353A GLY* 3.1 15.1 + - - -
354A HIS* 5.7 4.0 - - + +
373A GLN* 3.0 30.3 + - - +
403A TYR 3.9 1.0 + - - +
404A ASN* 1.3 76.0 - - - +
407A VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 407 (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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352A THR* 6.0 2.2 - - - -
404A ASN* 3.3 30.6 + - - +
406A ASN* 1.3 92.9 - - - +
408A ILE* 1.3 78.1 + - + +
409A ASN* 3.4 27.4 + - + +
440A GLU* 5.4 2.4 - - - +
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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