Contacts of the strand formed by residues 525 - 538 (chain B) in PDB entry 3GUT
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 PHE 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390B PRO* 3.9 17.5 - - + -
391B ALA* 3.6 27.4 - - - -
392B LYS* 3.7 40.8 + - + +
424B THR* 6.0 5.8 - - + -
478B ALA* 4.7 4.5 - - - +
517B PHE* 3.7 34.0 - - + +
518B LEU 3.9 7.0 - - - -
519B PRO* 3.8 15.3 - - + -
523B GLY 3.8 14.1 - - - -
524B SER* 1.3 66.9 - - - +
526B THR* 1.3 62.1 + - - +
527B ARG 3.8 0.4 - - - -
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Residues in contact with THR 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B ALA* 2.9 31.0 - - + +
479B GLU* 4.1 9.1 + - - +
480B GLY* 3.3 20.6 - - - +
517B PHE* 4.1 9.6 - - - -
520B ASP* 3.0 28.7 + - - +
524B SER* 2.7 22.7 + - - +
525B PHE* 1.3 76.8 - - - +
527B ARG* 1.3 65.6 + - - +
528B ARG* 3.2 9.4 + - - +
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Residues in contact with ARG 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PRO* 5.6 5.7 - - - +
387B TYR* 4.1 13.9 - - - -
516B ALA 3.5 1.6 - - - +
517B PHE* 3.0 4.8 - - - -
518B LEU* 2.6 82.1 + - + +
519B PRO* 3.1 22.6 + - - +
520B ASP* 4.2 15.9 - - + +
526B THR* 1.3 77.1 - - - +
528B ARG* 1.3 59.7 + - - +
529B LEU* 4.8 3.9 - - + +
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Residues in contact with ARG 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B GLY 5.4 0.4 - - - -
464B ASN* 2.7 45.0 - - - +
467B LEU* 4.0 21.1 - - - +
477B GLN* 3.5 27.5 + - - +
515B THR* 4.0 7.4 - - + -
516B ALA 3.5 3.8 - - - -
517B PHE* 3.5 28.7 - - + -
526B THR 3.2 6.2 + - - +
527B ARG* 1.3 70.3 - - - +
529B LEU* 1.3 72.1 + - - +
530B GLU* 4.3 5.2 + - - -
531B PRO* 3.2 23.2 - - - +
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B PRO* 3.3 34.3 - - + +
341B TYR* 3.6 27.8 - - - +
342B LEU* 4.9 1.1 - - + +
384B ILE* 4.5 10.3 - - + -
515B THR* 4.3 2.3 - - - +
516B ALA* 2.9 39.0 + - + +
518B LEU* 3.8 33.2 - - + -
527B ARG* 4.9 4.3 - - + +
528B ARG* 1.3 85.3 - - - +
530B GLU* 1.3 71.1 + - - +
531B PRO* 2.8 11.7 - - - +
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B PRO 5.4 1.6 + - - -
341B TYR* 5.7 6.6 - - + +
342B LEU* 4.1 18.0 + - - +
467B LEU* 5.0 7.3 - - - +
528B ARG* 4.3 5.6 + - - +
529B LEU* 1.3 70.2 - - - +
531B PRO* 1.3 90.2 - - - +
532B VAL* 3.7 1.7 + - - +
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Residues in contact with PRO 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B LEU* 5.6 0.7 - - + -
464B ASN* 3.5 16.6 - - - +
467B LEU* 4.1 9.9 - - + -
513B MET* 4.0 17.3 - - + -
514B PHE 3.2 8.1 - - - +
515B THR* 2.9 34.1 - - + +
516B ALA 5.3 0.2 - - - +
528B ARG* 3.2 22.7 - - - +
529B LEU 2.8 5.8 - - - +
530B GLU* 1.3 106.5 - - - +
532B VAL* 1.3 57.5 + - - +
533B VAL* 5.7 0.3 - - - +
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Residues in contact with VAL 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.3 44.0 - - + +
343B GLN* 4.8 0.7 - - - +
344B ILE* 4.3 20.4 - - + +
513B MET* 3.4 1.3 - - - -
514B PHE* 2.7 49.6 + - + +
530B GLU 4.7 2.2 - - - +
531B PRO* 1.3 76.9 - - - +
533B VAL* 1.3 78.6 + - + +
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ILE* 3.8 6.8 - - - +
347B GLN* 4.9 2.8 + - - -
398B VAL* 4.7 4.5 - - + -
404B ILE* 4.6 22.7 - - + -
511B ARG* 4.5 19.4 + - - +
512B LEU 3.3 5.4 - - - +
513B MET* 3.7 34.1 - - + -
531B PRO 5.7 0.4 - - - +
532B VAL* 1.3 87.1 - - + +
534B SER* 1.3 63.0 + - - +
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Residues in contact with SER 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 3.9 12.1 - - - +
347B GLN* 3.5 13.2 - - - -
348B PRO* 4.0 12.8 - - - +
511B ARG* 2.8 31.9 + - - -
512B LEU* 2.7 51.5 + - - +
514B PHE* 4.3 2.2 - - - -
533B VAL* 1.3 73.4 - - - +
535B ASP* 1.3 71.2 + - - +
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Residues in contact with ASP 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B GLN* 2.8 45.2 + - + +
348B PRO* 4.3 10.5 - - + +
350B GLN* 3.7 30.9 + - + +
511B ARG* 4.0 9.5 + - - +
534B SER* 1.3 92.7 + - - +
536B ALA* 1.3 63.4 + - - +
537B ILE* 3.9 1.2 + - - +
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Residues in contact with ALA 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B PRO* 5.8 0.2 - - - +
350B GLN* 3.4 26.3 + - - +
400B ASN* 3.8 31.2 - - - +
509B VAL* 4.0 8.3 - - + -
510B VAL 3.4 6.3 - - - +
511B ARG* 3.6 13.7 - - + +
534B SER 3.8 0.4 + - - -
535B ASP* 1.3 75.8 - - - +
537B ILE* 1.3 62.1 + - - +
538B TYR* 3.5 19.9 - - + +
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Residues in contact with ILE 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B PRO* 3.9 23.3 - - + -
349B LYS 4.4 8.3 - - - +
350B GLN 3.7 7.0 - - - +
353B PHE* 5.0 5.2 - - + -
355B PHE* 3.6 28.4 - - + -
367B LEU* 3.8 40.4 - - + -
439B ILE* 5.5 3.1 - - + -
509B VAL* 3.1 8.5 - - - +
510B VAL* 2.6 48.7 + - + +
511B ARG* 5.3 0.2 - - - -
512B LEU* 4.2 19.1 - - + -
535B ASP 4.4 1.8 - - - +
536B ALA* 1.3 78.1 - - - +
538B TYR* 1.3 66.4 + - - +
539B ASP 4.1 0.4 + - - -
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Residues in contact with TYR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B GLN* 3.1 35.4 + - + +
351B ARG* 3.7 49.3 + - + +
352B GLY 4.4 6.9 + - - -
353B PHE 3.8 5.7 + - - +
355B PHE* 4.3 2.2 - - - -
400B ASN* 4.8 6.6 + - - -
508B SER 3.6 4.5 - - - +
509B VAL* 3.9 24.9 - - + -
536B ALA* 3.5 29.8 - - + +
537B ILE* 1.3 77.1 - - - +
539B ASP* 1.3 66.5 + - - +
540B SER* 3.2 4.2 + - - -
544B ASN 5.8 0.9 - - - -
545B ALA* 4.3 13.3 - - + +
636B ASP* 6.2 0.9 - - + -
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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