Contacts of the strand formed by residues 420 - 429 (chain A) in PDB entry 3S3J
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 420 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A SER 3.6 15.3 - - - +
304A ALA* 4.4 10.1 - - + -
312A LEU* 4.4 19.3 - - + -
313A ILE* 6.4 0.7 - - + -
316A PHE* 5.1 6.7 - - + -
331A ILE* 4.2 33.2 - - + -
399A ALA* 4.3 13.2 - - + +
401A VAL* 3.8 31.8 - - + +
417A ASN* 3.8 3.9 + - - +
418A ARG* 3.1 7.1 - - - -
419A SER* 1.3 81.5 - - - +
421A ILE* 1.3 67.9 + - - +
422A VAL* 4.2 12.1 - - + -
575A TYR* 4.5 9.2 - - + -
281B LEU* 5.1 9.9 - - + +
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Residues in contact with ILE 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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302A ASN* 3.3 5.2 - - - +
303A SER* 2.8 60.0 + - - +
304A ALA* 4.6 1.8 - - - +
305A HIS* 4.8 8.3 - - + +
418A ARG* 3.4 25.4 - - + +
419A SER 4.0 2.9 - - - +
420A LEU* 1.3 86.1 - - - +
422A VAL* 1.3 68.0 + - - +
424A LEU* 3.9 28.3 - - + +
444A LYS* 5.9 0.9 - - - +
447A GLU* 6.0 2.0 - - - +
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASN* 3.2 17.7 - - + +
331A ILE* 4.5 13.0 - - + -
395A ALA 4.2 3.1 - - - +
396A GLU 3.1 33.9 - - - +
397A VAL 3.5 8.9 - - - +
398A ASN* 3.8 5.5 - - - +
399A ALA* 3.3 36.2 + - + +
420A LEU* 4.2 15.0 - - + -
421A ILE* 1.3 84.1 - - - +
423A GLY* 1.3 61.8 + - - +
424A LEU 4.0 0.4 - - - -
444A LYS* 2.8 20.3 + - - -
573A ASN* 4.8 0.7 - - - +
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Residues in contact with GLY 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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300A ASN* 2.9 17.5 - - - -
301A TYR 3.3 0.6 + - - -
302A ASN* 3.1 11.9 + - - -
397A VAL* 3.8 14.8 - - - -
422A VAL* 1.3 72.9 - - - +
424A LEU* 1.3 67.4 + - - +
426A ILE* 4.7 4.9 - - - -
440A THR* 4.3 6.4 - - - +
444A LYS* 3.1 27.7 + - - +
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Residues in contact with LEU 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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172A ALA* 4.4 12.3 - - + -
300A ASN* 3.3 1.5 + - - +
301A TYR* 2.8 42.6 + - + +
302A ASN 4.2 1.6 - - - -
303A SER* 3.4 33.0 - - - +
421A ILE* 3.9 31.4 - - + +
423A GLY* 1.3 79.5 - - - +
425A LYS* 1.3 76.4 + - + +
426A ILE 2.9 4.6 + - - -
440A THR* 4.2 1.8 - - - -
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Residues in contact with LYS 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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172A ALA* 4.6 19.7 + - + +
175A ILE* 4.1 13.9 - - + +
301A TYR* 3.3 21.2 - - + -
424A LEU* 1.3 80.0 - - + +
426A ILE* 1.3 57.8 + - - +
427A SER* 2.5 26.1 + - - -
436A ARG* 3.6 26.3 - - - +
438A ASP* 3.7 9.8 + - - +
440A THR* 3.4 13.8 + - - +
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Residues in contact with ILE 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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298A VAL* 4.7 7.6 - - + -
299A THR 3.1 16.2 - - - +
300A ASN* 3.6 27.4 - - + +
337A TRP* 5.1 1.8 - - + -
397A VAL* 4.0 14.1 - - + -
423A GLY* 4.9 2.9 - - - -
424A LEU 3.9 3.8 - - - +
425A LYS* 1.3 71.6 - - - +
427A SER* 1.3 60.4 + - - +
438A ASP* 3.4 6.2 - - - +
439A ILE* 2.8 47.1 + - + -
440A THR* 3.0 30.7 + - + +
443A TYR* 3.9 38.8 - - + -
444A LYS* 4.9 1.6 - - + -
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Residues in contact with SER 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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168A TYR* 4.3 18.9 - - - -
297A VAL 4.0 0.7 - - - +
298A VAL* 3.3 6.7 - - - -
299A THR* 2.7 40.8 + - - -
301A TYR* 4.0 6.3 - - - -
425A LYS 2.5 20.8 + - - -
426A ILE* 1.3 74.9 + - - +
428A THR* 1.3 60.9 + - - +
436A ARG* 2.7 38.1 + - - -
437A GLU 3.3 4.3 - - - -
439A ILE* 4.8 1.6 - - - -
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Residues in contact with THR 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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168A TYR* 3.7 10.3 - - - -
296A ARG* 3.7 48.4 - - - +
297A VAL 2.8 22.1 + - - -
298A VAL* 4.0 8.1 - - - -
427A SER* 1.3 77.5 - - - +
429A LYS* 1.3 67.0 + - - +
436A ARG 3.7 0.7 - - - -
437A GLU* 2.7 40.7 + - + +
439A ILE* 4.1 17.3 - - + -
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Residues in contact with LYS 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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158A GLU* 2.7 31.6 + - - +
159A TYR* 4.9 11.1 + - - -
164A GLN 4.6 0.2 - - - -
165A GLY* 3.8 7.6 - - - -
166A PHE* 3.7 46.1 + - + +
168A TYR* 3.6 13.8 - - + +
297A VAL 4.8 0.8 + - - -
428A THR* 1.3 87.2 + - - +
430A SER* 1.3 79.7 + - - +
431A VAL 3.7 1.0 + - - -
433A ARG 3.2 8.4 + - - +
434A ASP* 4.3 0.4 - - - -
435A GLU 3.7 7.0 - - - +
437A GLU* 4.6 2.1 - - - +
707A GOL 3.0 50.6 - - - -
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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