Contacts of the strand formed by residues 428 - 437 (chain A) in PDB entry 1W21
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 PRO 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.1 17.5 - - + -
98A CYS 4.1 6.3 - - - +
100A VAL* 3.8 17.9 - - + -
103A TRP* 3.5 13.5 - - + -
361A PHE* 3.7 46.2 - - + -
366A ASN* 5.6 0.4 - - - +
417A ILE* 4.1 3.8 - - + -
426A PHE 3.2 9.6 - - - +
427A ASN* 1.3 94.7 - - - +
429A CYS* 1.3 58.8 + - - +
455A CYS* 3.2 3.1 - - - +
456A GLY 2.8 30.0 + - - -
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Residues in contact with CYS 429 (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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103A TRP* 4.6 0.2 - - - -
106A LEU* 4.7 0.2 - - - -
361A PHE* 3.1 17.7 - - - -
416A PHE* 3.0 57.9 + - + +
418A ASP* 4.7 11.9 - - - -
427A ASN* 3.7 10.5 - - - -
428A PRO* 1.3 76.3 - - - +
430A PHE* 1.3 65.2 + - - +
454A LEU 3.2 5.4 - - - +
455A CYS* 2.0 46.0 - - - +
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Residues in contact with PHE 430 (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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103A TRP* 3.5 44.9 - + - -
359A PHE* 3.4 33.4 - + + -
381A TYR* 4.6 1.3 - + - -
383A MET* 3.7 26.2 - - + -
403A ILE* 3.8 19.7 - - + -
414A GLY 3.2 15.3 - - - +
416A PHE* 3.7 7.6 - - - -
429A CYS* 1.3 77.0 - - - +
431A TYR* 1.3 71.6 + - - +
432A VAL* 3.7 20.9 - - + -
453A ALA* 3.2 4.3 - - - +
454A LEU* 2.9 57.8 + - + -
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Residues in contact with TYR 431 (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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126A PRO* 2.9 36.6 + - + -
127A TYR* 3.3 24.9 - - + -
128A LEU* 4.1 22.9 - - + -
234A GLU 3.3 5.7 + - - -
235A SER* 3.5 4.2 - - - -
357A LYS* 3.0 32.1 - - - +
412A TYR* 4.3 6.1 - - + +
413A SER* 3.2 31.8 - - - -
414A GLY* 3.1 36.7 + - - -
415A ALA 4.3 1.8 - - - -
416A PHE* 4.4 6.5 - + + -
430A PHE* 1.3 78.4 - - - +
432A VAL* 1.3 75.8 + - - +
433A GLU* 4.1 1.3 - - + -
451A ILE* 4.3 3.6 - - + -
452A VAL 3.2 13.7 - - - +
453A ALA* 4.1 1.6 - - + +
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Residues in contact with VAL 432 (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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381A TYR* 3.9 33.4 - - + -
403A ILE* 4.2 13.7 - - + -
404A VAL* 4.4 0.9 - - + -
410A SER* 3.9 17.7 - - - -
412A TYR 3.6 6.5 - - - +
413A SER* 4.4 0.2 - - - +
430A PHE* 3.7 22.2 - - + -
431A TYR* 1.3 83.2 - - - +
433A GLU* 1.3 72.8 + - - +
434A LEU* 3.6 15.5 + - + +
451A ILE* 3.8 3.6 - - - +
452A VAL* 3.1 38.2 + - + +
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Residues in contact with GLU 433 (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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124A ARG* 2.8 43.8 + - - +
125A GLU 3.0 16.8 + - - -
126A PRO* 3.3 33.0 - - + +
410A SER* 2.9 26.3 - - - -
411A GLY 3.1 3.5 + - - -
412A TYR* 2.8 44.7 + - + +
431A TYR* 4.1 2.3 - - + -
432A VAL* 1.3 73.7 - - - +
434A LEU* 1.3 60.6 + - - +
435A ILE* 3.6 8.7 - - + +
449A ASN* 3.6 12.3 - - + -
450A SER 3.9 4.0 - - - -
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Residues in contact with LEU 434 (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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108A LYS* 4.6 3.1 - - - +
404A VAL* 3.8 29.8 - - + -
409A TRP 3.9 16.4 - - - +
410A SER* 3.9 2.0 - - - -
432A VAL* 3.8 23.1 - - + +
433A GLU* 1.3 72.9 - - - +
435A ILE* 1.3 62.3 + - - +
436A ARG* 3.5 6.4 + - - +
449A ASN* 3.1 22.2 - - - -
450A SER* 3.0 35.0 + - - +
451A ILE 4.4 0.9 - - - -
452A VAL* 4.1 18.4 - - + +
466A TRP 3.4 21.8 - - - +
467A HIS 3.9 0.9 - - - +
468A ASP* 3.7 21.8 - - + +
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Residues in contact with ILE 435 (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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124A ARG* 3.7 22.0 - - - +
378A ARG* 4.3 15.9 - - + +
409A TRP* 3.1 29.5 + - + +
410A SER 2.9 15.7 + - - +
411A GLY* 3.7 14.4 - - - -
433A GLU* 3.6 34.3 - - + +
434A LEU* 1.3 69.5 - - - +
436A ARG* 1.3 76.0 + - - +
437A GLY 5.4 1.1 - - - +
438A ARG 4.3 7.0 - - - +
439A PRO* 5.8 1.6 - - + -
447A THR* 4.0 17.0 - - + -
448A SER 3.5 12.8 - - - +
449A ASN* 4.1 0.2 - - - -
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Residues in contact with ARG 436 (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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112A ILE* 4.0 13.5 - - + -
408A ASN* 5.6 6.1 - - - +
409A TRP* 4.1 11.2 - - - +
434A LEU 3.5 3.8 + - - +
435A ILE* 1.3 90.0 - - - +
437A GLY* 1.3 62.6 + - - +
441A GLU* 2.7 39.0 + - - +
446A TRP* 3.4 21.4 - - + -
447A THR* 3.5 2.4 - - - -
448A SER 3.0 32.1 + - - +
468A ASP* 2.8 57.8 + - - +
469A GLY 4.4 1.2 - - - +
470A ALA* 2.9 33.1 + - - +
472A ILE* 3.9 19.2 - - + +
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Residues in contact with GLY 437 (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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435A ILE* 5.4 0.9 - - - +
436A ARG* 1.3 74.8 - - - +
438A ARG* 1.3 61.3 + - - +
440A LYS* 3.5 4.0 + - - +
441A GLU* 2.6 47.9 + - - +
444A VAL* 3.6 20.0 - - - -
446A TRP* 3.3 13.3 - - - -
472A ILE* 4.5 0.4 - - - +
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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