Contacts of the strand formed by residues 351 - 361 (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 VAL 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A LYS 4.4 0.9 - - - +
350A LYS* 1.3 81.5 - - - +
352A THR* 1.3 76.1 + - - +
375A THR* 3.3 9.2 - - - +
376A LEU* 2.7 42.3 + - + -
402A TRP* 3.4 37.0 - - + -
404A ASN* 4.4 5.8 - - - +
413A PRO* 3.5 34.1 - - + -
415A VAL* 4.0 13.5 - - + -
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Residues in contact with THR 352 (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* 1.3 82.2 + - - +
353A GLY* 1.3 59.3 + - - +
373A GLN* 5.4 0.2 - - - +
374A GLY* 3.4 21.5 - - - +
375A THR* 4.2 11.1 + - - +
404A ASN* 2.8 30.7 + - - +
406A ASN* 3.1 28.1 + - - +
407A VAL* 6.0 2.7 - - - -
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Residues in contact with GLY 353 (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* 4.1 5.1 - - - +
352A THR* 1.3 73.4 - - - +
354A HIS* 1.3 58.1 + - - -
372A PHE 4.0 0.5 - - - +
373A GLN* 3.2 6.6 - - - -
374A GLY 2.8 32.2 + - - +
376A LEU* 4.1 11.0 - - - +
403A TYR 3.0 15.3 - - - -
404A ASN* 4.4 0.2 - - - -
406A ASN* 3.1 15.2 + - - -
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Residues in contact with HIS 354 (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* 1.3 73.4 - - - -
355A VAL* 1.3 62.8 + - - +
356A LEU* 3.6 31.0 - - + +
370A GLU* 3.3 21.5 - - - +
372A PHE 3.0 13.2 - - - +
373A GLN* 2.7 30.7 + - - +
402A TRP* 3.2 6.4 - - - +
403A TYR* 3.0 51.8 + + + +
406A ASN* 5.4 4.1 + - + +
80B LYS* 6.2 3.6 - - + -
81B GLY* 5.5 4.4 + - - -
83B GLU* 3.4 27.3 + - - -
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Residues in contact with VAL 355 (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 24.0 - - + -
346A LEU* 4.4 7.4 - - + -
354A HIS* 1.3 76.5 - - - +
356A LEU* 1.3 60.3 - - - +
357A VAL* 4.9 0.7 - - + -
370A GLU* 3.5 3.5 - - - +
371A ILE* 2.9 34.8 + - + -
372A PHE* 2.8 16.5 + - + +
376A LEU* 3.7 33.0 - - + -
382A TYR* 6.3 0.7 - - + -
400A PHE* 3.7 35.0 - - + -
401A ILE 3.7 2.5 - - - -
402A TRP* 3.9 7.4 - - + -
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Residues in contact with LEU 356 (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 HIS* 3.6 21.5 - - + +
355A VAL* 1.3 75.2 - - - +
357A VAL* 1.3 68.5 + - - +
368A GLN* 4.1 22.2 - - + +
369A TYR* 3.0 9.4 - - - +
370A GLU* 3.5 34.1 - - + +
400A PHE* 3.6 2.3 - - - -
401A ILE* 3.0 48.5 + - + +
403A TYR* 3.6 36.6 - - + -
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Residues in contact with VAL 357 (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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342A VAL* 4.3 20.2 - - + -
344A VAL* 5.0 3.6 - - + -
355A VAL* 4.9 3.8 - - + -
356A LEU* 1.3 79.9 - - - +
358A SER* 1.3 64.1 + - - +
359A LEU* 4.3 11.2 - - + -
367A ARG 3.9 0.7 - - - +
368A GLN* 3.4 4.1 - - - -
369A TYR* 2.9 31.4 + - - +
371A ILE* 4.0 24.7 - - + -
386A PHE* 5.4 3.7 - - + -
398A VAL* 3.7 26.7 - - + -
399A LYS 3.2 6.7 - - - +
400A PHE* 4.4 8.3 - - + -
420A ILE* 4.1 19.3 - - + -
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Residues in contact with SER 358 (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* 1.3 74.8 - - - +
359A LEU* 1.3 64.1 + - - +
360A PHE* 3.1 25.3 - - - -
366A SER* 4.0 7.9 - - - -
367A ARG 3.8 15.9 - - - -
368A GLN* 3.9 19.6 + - - +
398A VAL* 3.4 5.2 - - - +
399A LYS* 2.9 44.8 + - - +
443A LEU* 5.0 0.5 - - - +
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Residues in contact with LEU 359 (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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340A TYR* 3.8 46.7 - - + -
342A VAL* 4.2 14.1 - - + -
357A VAL* 4.3 6.7 - - + -
358A SER* 1.3 73.2 - - - +
360A PHE* 1.3 62.7 + - - +
361A GLY 4.2 0.7 - - - -
365A ASN* 3.0 7.3 - - - +
366A SER* 2.9 39.8 + - - +
386A PHE* 4.2 14.1 - - + -
392A VAL* 3.9 15.8 - - + +
395A LEU* 4.2 9.2 - - + -
397A LYS 4.1 3.1 - - - -
398A VAL* 3.9 18.4 - - + -
422A VAL* 4.1 20.4 - - + -
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Residues in contact with PHE 360 (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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358A SER* 3.1 37.7 - - - -
359A LEU* 1.3 76.7 - - - +
361A GLY* 1.3 59.3 + - - +
365A ASN* 3.4 39.9 - - + -
366A SER 5.3 0.9 - - - -
392A VAL* 4.8 1.3 - - - -
395A LEU* 3.8 3.1 - - - +
396A GLU* 2.9 23.9 + - + +
397A LYS* 2.9 47.4 + - + +
399A LYS* 3.4 41.3 - - + -
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Residues in contact with GLY 361 (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* 1.3 74.7 - - - +
362A ASN* 1.3 64.7 + - - -
363A LYS 3.3 2.7 - - - -
364A GLY 3.0 17.4 + - - +
392A VAL* 3.4 14.8 - - - +
394A ASP 3.1 15.9 - - - -
395A LEU* 3.9 3.1 - - - -
396A GLU* 3.9 14.2 - - - +
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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