Contacts of the strand formed by residues 419 - 429 (chain A) in PDB entry 3CL0
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 ARG 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A CYS* 3.9 12.5 - - - +
411A VAL* 3.4 7.8 - - - +
412A GLN* 3.0 64.9 + - + +
413A THR* 4.9 4.0 - - + +
415A LEU* 3.8 33.0 - - + +
417A CYS 3.7 1.0 + - - -
418A ILE* 1.3 69.2 - - - +
420A PRO* 1.3 80.9 - - + +
421A CYS* 3.7 12.6 + - - -
447A CYS* 4.0 8.7 - - - +
448A GLY 3.4 20.8 + - - +
449A VAL* 4.7 13.5 - - - +
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Residues in contact with PRO 420 (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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91A LEU* 4.5 5.8 - - + -
92A CYS* 4.4 5.2 - - + +
94A ILE* 4.2 27.1 - - + -
97A TRP* 3.5 4.8 - - + -
354A PHE* 3.7 35.4 - - + -
356A TYR* 3.4 25.8 - - + +
410A PHE 4.1 3.4 - - - +
411A VAL* 4.4 2.7 - - + -
418A ILE 3.6 8.3 - - - +
419A ARG* 1.3 86.9 - - + +
421A CYS* 1.3 56.2 + - - +
448A GLY* 2.7 32.4 + - - -
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Residues in contact with CYS 421 (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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97A TRP* 4.2 2.2 - - - -
354A PHE* 3.4 12.8 - - - -
410A PHE* 2.8 57.4 + - + +
412A GLN* 4.1 9.9 - - - -
419A ARG* 3.8 14.4 - - - -
420A PRO* 1.3 75.7 - - - +
422A PHE* 1.3 62.6 + - - +
446A PHE 3.2 7.6 - - - +
447A CYS* 2.1 48.5 - - - +
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Residues in contact with PHE 422 (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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97A TRP* 3.7 27.4 - + - -
352A PHE* 3.3 38.8 - + + -
374A PHE* 3.8 10.5 - + - -
376A MET* 3.6 30.7 - - + -
397A ILE* 4.0 8.3 - - + -
408A GLY 3.2 12.3 - - - +
410A PHE* 3.6 6.3 - - - -
421A CYS* 1.3 74.3 - - - +
423A TRP* 1.3 61.8 + - - +
424A VAL* 3.7 27.4 - - + -
445A SER* 3.3 3.5 - - - -
446A PHE* 2.9 70.7 + + + +
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Residues in contact with TRP 423 (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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120A PRO* 3.1 29.2 - - + -
121A PHE* 3.5 23.2 - - + +
122A ILE* 3.5 37.5 + - + +
227A GLU 3.7 9.4 - - - -
228A SER* 4.0 3.0 - - - -
350A LYS* 3.9 11.7 - - + -
406A TYR* 3.6 22.2 - + + -
407A SER* 3.2 31.2 - - - -
408A GLY* 3.1 53.2 + - - -
409A SER 4.1 6.4 + - - -
410A PHE* 3.8 14.1 - + - -
422A PHE* 1.3 74.0 - - - +
424A VAL* 1.3 68.7 + - - +
425A GLU* 3.6 13.0 - - + -
443A SER* 5.4 4.9 - - - -
444A ILE 3.3 11.9 - - - +
445A SER* 4.1 0.2 - - - +
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Residues in contact with VAL 424 (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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374A PHE* 3.9 31.2 - - + -
397A ILE* 4.5 0.4 - - + -
404A SER* 4.1 14.1 - - - -
405A GLY 4.5 0.7 - - - +
406A TYR 3.5 8.7 - - - +
422A PHE* 3.7 24.9 - - + -
423A TRP* 1.3 83.1 - - - +
425A GLU* 1.3 73.6 + - - +
426A LEU* 3.8 14.4 + - + -
443A SER* 3.4 6.2 - - - -
444A ILE* 2.9 51.4 + - + +
446A PHE* 5.2 0.2 - - + -
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Residues in contact with GLU 425 (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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118A ARG* 2.8 50.2 + - - +
119A GLU 2.9 19.9 + - - -
120A PRO* 3.3 27.8 - - + +
404A SER 3.2 0.9 - - - -
405A GLY* 2.9 26.7 + - - -
406A TYR* 2.7 37.4 + - + +
423A TRP* 3.6 4.5 - - + -
424A VAL* 1.3 74.0 - - - +
426A LEU* 1.3 63.1 + - - +
427A ILE* 3.4 13.7 - - + +
441A GLY* 4.5 6.1 - - - -
442A SER 3.5 6.7 - - - +
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Residues in contact with LEU 426 (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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102A LYS* 5.0 1.3 - - - +
398A VAL* 3.9 23.8 - - + -
403A TRP 3.6 24.0 - - - +
404A SER* 4.0 9.2 - - - +
424A VAL* 4.0 16.4 - - + +
425A GLU* 1.3 71.1 - - - +
427A ILE* 1.3 64.3 + - - +
428A ARG* 3.7 8.6 + - - +
441A GLY* 3.4 2.2 - - - -
442A SER* 2.8 48.3 + - - +
443A SER 4.8 0.4 - - - -
444A ILE* 4.0 20.2 - - + +
458A TRP 3.8 13.9 - - - +
459A PRO 3.9 0.7 - - - +
460A ASP* 3.6 29.6 - - + +
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Residues in contact with ILE 427 (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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118A ARG* 3.5 22.9 - - - +
371A ARG* 4.0 19.1 - - + +
403A TRP* 3.3 18.0 - - - +
404A SER 3.3 13.1 + - - +
405A GLY* 3.8 15.9 - - - -
406A TYR 4.4 0.2 - - - +
425A GLU* 3.4 35.2 - - + +
426A LEU* 1.3 71.1 - - - +
428A ARG* 1.3 74.0 + - - +
430A ARG 4.6 5.2 - - - +
431A PRO* 6.1 1.1 - - + -
433A GLU* 4.6 0.2 - - - +
439A THR* 3.7 22.9 - - + -
440A SER 3.4 12.6 - - - +
441A GLY* 4.2 0.7 - - - -
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Residues in contact with ARG 428 (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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106A ILE* 3.6 18.8 - - + -
403A TRP* 3.7 18.1 - - - -
426A LEU 3.9 1.1 - - - +
427A ILE* 1.3 87.1 - - - +
429A GLY* 1.3 60.7 + - - +
433A GLU* 2.6 35.3 + - - -
438A TRP* 3.6 8.6 - - + -
439A THR* 3.5 4.2 - - - +
440A SER 2.8 32.1 + - - -
460A ASP* 2.8 60.5 + - - +
461A GLY* 4.2 2.4 - - - +
462A ALA* 2.8 33.9 + - - +
464A LEU* 3.4 24.4 - - + +
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Residues in contact with GLY 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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428A ARG* 1.3 73.1 - - - +
430A ARG* 1.3 66.8 + - - +
432A LYS* 3.4 3.6 + - - +
433A GLU* 2.8 39.8 + - - +
436A THR* 3.2 19.5 - - - -
438A TRP* 3.4 4.9 - - - -
464A LEU* 3.5 12.7 - - - +
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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