Contacts of the strand formed by residues 438 - 449 (chain A) in PDB entry 1P9W
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 TYR 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ARG* 3.3 62.1 + - + +
395A THR 3.5 6.1 - - - +
396A LEU* 3.6 37.2 - - + -
397A CYS 3.7 0.2 - - - +
427A ALA* 3.5 21.9 - - + +
433A CYS* 3.5 15.2 - - - +
434A ASN 5.0 0.5 + - - -
435A HIS 5.0 3.7 - - - +
436A LYS* 3.3 42.2 + - + +
437A GLY* 1.3 75.1 - - - +
439A ARG* 1.3 59.8 + - - +
440A GLY 5.0 0.4 - - - +
491A THR* 4.5 2.0 - - - -
492A SER* 3.2 28.4 + - - -
494A GLU* 4.1 5.5 + - - +
495A GLU* 4.4 7.2 + - + +
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Residues in contact with ARG 439 (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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395A THR* 2.7 27.5 + - - +
396A LEU 4.5 2.1 - - - +
397A CYS* 3.8 22.5 - - + +
398A PRO* 3.8 30.0 - - + +
399A ASP* 4.2 11.1 + - - -
432A LYS* 3.9 27.7 + - - +
433A CYS* 4.9 1.3 - - + -
438A TYR* 1.3 73.7 - - - +
440A GLY* 1.3 64.9 + - - +
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Residues in contact with GLY 440 (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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394A ARG* 3.6 8.3 - - - +
395A THR* 2.9 23.0 + - - +
438A TYR 4.4 0.9 + - - -
439A ARG* 1.3 77.2 - - - +
441A ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 441 (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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227A LEU* 6.1 3.8 - - - +
392A LEU* 3.6 25.2 - - + +
393A VAL 3.2 16.2 - - - +
394A ARG* 3.9 13.2 - - - -
395A THR* 3.2 8.0 + - - +
440A GLY* 1.3 76.6 - - - +
442A THR* 1.3 65.5 + - - +
701A ANP 2.6 79.9 + - + +
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Residues in contact with THR 442 (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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238A SER 5.4 0.3 + - - -
239A LEU 3.7 1.9 + - - -
240A GLY* 3.5 13.7 + - - -
392A LEU* 3.5 8.9 - - - -
393A VAL* 2.8 45.8 + - + +
395A THR* 3.7 22.6 - - + +
441A ARG* 1.3 77.1 - - - +
443A GLY* 1.3 64.6 + - - +
485A LYS* 3.3 32.4 + - + +
490A ILE* 4.5 4.5 - - + -
701A ANP 3.9 6.5 + - - -
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Residues in contact with GLY 443 (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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239A LEU 3.1 21.2 + - - -
240A GLY 3.6 5.5 - - - +
390A GLN* 5.4 1.1 - - - -
391A ARG 3.4 8.5 - - - -
392A LEU* 4.0 7.9 - - - -
442A THR* 1.3 74.9 - - - +
444A ILE* 1.3 62.5 + - - +
445A HIS* 3.5 13.5 - - - -
485A LYS* 3.0 25.5 + - - -
701A ANP 3.8 3.1 + - - -
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Residues in contact with ILE 444 (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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390A GLN* 3.5 3.1 - - - -
391A ARG* 3.0 60.4 + - + +
393A VAL* 3.7 32.5 - - + -
443A GLY* 1.3 77.7 - - - +
445A HIS* 1.3 63.7 + - - +
478A ILE* 3.9 15.2 - - + +
479A ARG* 5.7 0.2 - - - -
481A ASP* 3.2 13.9 - - + +
482A GLY* 3.7 34.5 - - - +
485A LYS* 4.2 16.4 - - + -
496A VAL* 4.6 8.1 - - + +
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Residues in contact with HIS 445 (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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239A LEU* 3.9 17.2 + - - +
241A MSE 3.5 39.3 - - + +
245A ASN* 3.9 17.4 + - - +
388A LEU* 3.8 22.2 - - + -
389A ALA 3.3 7.6 - - - +
390A GLN* 3.6 39.3 + - + +
443A GLY* 3.5 30.1 + - - -
444A ILE* 1.3 73.2 - - - +
446A GLU* 1.3 61.0 + - - +
476A PRO 4.8 1.2 - - - +
477A SER 4.5 1.0 - - - +
478A ILE* 3.7 7.7 + - - +
481A ASP* 2.8 35.5 + - - +
701A ANP 5.7 0.4 + - - -
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Residues in contact with GLU 446 (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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245A ASN* 5.2 0.9 - - - -
362A THR* 5.8 2.1 - - - -
363A ALA* 3.7 26.5 + - + +
364A VAL* 5.1 4.0 + - - +
387A VAL 3.5 4.2 - - - +
388A LEU* 3.6 3.8 - - - -
389A ALA* 2.9 36.0 + - + +
445A HIS* 1.3 75.8 - - - +
447A LEU* 1.3 64.0 + - - +
448A LEU* 4.9 0.8 - - + +
468A GLU* 5.1 2.6 - - - +
471A ILE* 4.6 7.1 - - - +
472A ARG* 3.0 31.2 + - - -
475A THR* 4.7 6.3 - - - +
476A PRO 3.9 12.8 - - - +
477A SER* 3.9 1.7 - - - -
478A ILE* 3.2 40.4 + - + +
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Residues in contact with LEU 447 (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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241A MSE 4.8 1.3 - - + -
245A ASN* 3.7 29.7 + - - +
248A ASN* 3.6 33.9 - - + +
249A PHE* 3.6 27.8 - - + +
252A LEU* 4.6 7.4 - - + -
260A ILE* 6.4 0.2 - - + -
387A VAL 4.0 9.0 - - - +
388A LEU* 4.0 23.3 - - + -
446A GLU* 1.3 75.9 - - - +
448A LEU* 1.3 68.7 + - - +
449A LEU* 3.5 21.1 + - + +
475A THR* 3.7 22.4 + - - +
476A PRO 5.3 0.6 + - - -
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Residues in contact with LEU 448 (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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363A ALA* 4.1 25.1 - - + +
364A VAL* 4.0 20.6 - - + -
367A VAL* 5.8 1.6 - - + -
384A LEU* 4.6 4.9 - - + -
386A GLY* 3.2 7.8 - - - -
387A VAL* 3.0 54.6 + - + +
446A GLU* 3.8 3.3 + - - +
447A LEU* 1.3 72.0 - - - +
449A LEU* 1.3 64.0 + - - +
450A VAL* 4.0 23.6 - - + -
454A LEU* 4.1 5.8 - - + -
467A MSE 4.7 5.2 - - + -
471A ILE* 3.5 38.1 - - + -
475A THR* 5.1 2.2 - - - -
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Residues in contact with LEU 449 (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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248A ASN* 4.0 36.1 - - + +
252A LEU* 3.8 33.7 - - + -
385A LEU 4.1 1.1 - - - +
447A LEU* 3.5 25.8 + - + +
448A LEU* 1.3 79.5 - - - +
450A VAL* 1.3 67.1 + - - +
451A ASP* 3.5 8.0 + - - +
454A LEU* 3.8 11.2 - - - +
471A ILE* 5.1 4.1 - - - +
475A THR* 5.0 11.3 - - + +
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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