Contacts of the strand formed by residues 553 - 563 (chain B) in PDB entry 2O1X
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 ALA 553 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506B ASP* 5.2 0.7 - - + -
507B ASP 3.7 16.2 - - - +
509B VAL* 4.2 14.4 - - + -
549B VAL 3.3 18.4 + - - +
550B GLY* 4.6 1.6 - - - +
551B GLY 3.8 1.7 - - - -
552B ARG* 1.3 78.3 - - - +
554B ARG* 1.3 66.6 - - - +
555B ALA 3.4 12.7 + - - +
556B LEU* 4.2 9.9 - - + -
583B PRO* 4.1 14.6 - - - +
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Residues in contact with ARG 554 (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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507B ASP* 2.7 61.4 + - - +
508B VAL* 3.8 14.1 - - - +
553B ALA* 1.3 72.8 - - - +
555B ALA* 1.3 62.2 + - + +
583B PRO* 4.6 1.2 - - - +
584B THR* 3.6 17.5 + - - -
621B LEU* 2.4 36.8 + - - +
622B GLY* 3.8 13.3 - - - -
623B VAL 4.2 0.4 - - - +
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Residues in contact with ALA 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B ASP 3.2 3.2 + - - +
508B VAL* 3.4 13.4 - - + -
509B VAL 3.2 20.4 + - - -
553B ALA* 3.2 3.8 - - - +
554B ARG* 1.3 84.6 - - + +
556B LEU* 1.3 69.3 + - - +
583B PRO* 4.9 0.2 - - - -
584B THR* 3.1 17.7 - - + +
621B LEU* 3.6 38.4 - - + -
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Residues in contact with LEU 556 (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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508B VAL* 5.1 0.2 - - - -
509B VAL* 3.4 16.6 - - + +
511B LEU* 4.9 12.1 - - + -
546B LEU* 4.7 12.6 - - + -
549B VAL* 3.7 36.1 - - + +
550B GLY* 4.1 11.4 - - - -
553B ALA* 4.2 2.5 - - + -
555B ALA* 1.3 84.2 - - - +
557B ILE* 1.3 67.6 + - - +
558B THR* 5.4 0.4 - - + -
572B VAL* 5.1 2.0 - - + -
576B LEU* 4.1 13.5 - - + -
583B PRO* 3.7 28.7 - - + -
584B THR 2.6 13.7 + - - +
585B VAL* 3.2 12.9 - - + -
586B ARG* 2.8 25.6 + - - +
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Residues in contact with ILE 557 (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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508B VAL* 4.3 5.8 - - + -
509B VAL 3.0 6.1 + - - +
510B ILE* 3.4 16.3 - - + +
511B LEU* 2.8 27.0 + - - +
556B LEU* 1.3 79.2 - - - +
558B THR* 1.3 66.4 + - - +
559B VAL* 3.8 13.9 - - + -
586B ARG* 3.5 11.2 - - + +
588B LEU* 3.7 27.6 - - + -
614B ILE* 4.4 7.0 - - + +
617B VAL* 3.7 23.3 - - + -
618B LEU* 3.8 33.7 - - + +
621B LEU* 3.9 15.9 - - + -
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Residues in contact with THR 558 (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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511B LEU* 3.3 26.9 - - + -
556B LEU* 5.4 1.1 - - + -
557B ILE* 1.3 77.6 - - - +
559B VAL* 1.3 66.1 + - - +
560B GLU* 6.0 0.4 - - - -
568B PHE* 3.5 21.5 - - + -
569B GLY* 3.7 8.3 - - - -
572B VAL* 3.9 20.9 - - + -
585B VAL* 4.5 9.4 - - + +
586B ARG 3.0 5.8 + - - +
587B VAL* 3.5 23.6 - - - +
588B LEU* 3.0 27.6 + - - +
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Residues in contact with VAL 559 (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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510B ILE* 3.8 25.8 - - + -
511B LEU 3.0 6.3 + - - +
512B ALA* 3.4 22.1 - - + +
513B GLY 4.3 1.2 + - - -
516B ALA* 3.3 23.6 - - + +
557B ILE* 3.8 11.4 - - + -
558B THR* 1.3 79.8 - - - +
560B GLU* 1.3 65.2 + - - +
568B PHE* 4.0 5.3 - - - -
588B LEU* 3.4 6.5 - - + +
609B ILE* 3.7 41.7 - - + +
614B ILE* 4.0 16.2 - - + -
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Residues in contact with GLU 560 (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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440B LEU* 4.2 6.1 - - + +
453B LEU* 6.3 2.0 - - - -
516B ALA* 4.1 5.2 - - - -
558B THR 6.0 0.2 - - - -
559B VAL* 1.3 77.4 - - - +
561B ASP* 1.3 58.7 + - - +
562B ASN* 3.0 31.1 + - + +
563B THR 3.4 17.5 - - - +
564B VAL* 4.1 9.5 - - - +
567B GLY* 3.3 8.3 - - - -
568B PHE* 2.6 38.7 + - + +
569B GLY* 2.9 25.8 + - - -
587B VAL* 4.3 4.3 - - - +
588B LEU 3.2 11.8 + - - +
589B GLY* 3.5 16.1 - - - -
590B ILE* 3.9 2.1 - - - +
609B ILE* 4.1 6.2 - - - +
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Residues in contact with ASP 561 (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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424B ALA 3.5 6.9 - - - +
425B GLY* 3.0 25.1 - - - -
426B ILE 3.2 15.8 + - - +
440B LEU* 5.3 1.4 - - - +
453B LEU* 6.0 3.4 - - + +
477B ARG* 2.4 37.5 + - - +
479B PRO* 4.8 1.0 - - - +
513B GLY 5.7 0.4 + - - -
515B LYS* 4.0 27.1 - - + +
516B ALA* 4.3 7.9 - - + +
560B GLU* 1.3 69.8 - - - +
562B ASN* 1.3 54.6 + - - +
590B ILE* 3.7 7.3 - - - +
604B HIS* 2.7 39.4 + - + +
609B ILE* 4.5 5.6 - - + -
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Residues in contact with ASN 562 (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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437B VAL* 3.4 17.4 + - - +
438B PHE 3.6 1.4 - - - -
439B ASP* 3.6 6.6 - - - +
440B LEU* 2.9 49.9 + - + +
441B SER* 3.3 20.4 + - - -
477B ARG* 3.9 0.4 + - - +
560B GLU* 3.0 25.9 + - + +
561B ASP* 1.3 77.6 - - - +
563B THR* 1.3 96.0 + - - +
567B GLY* 4.0 1.2 - - - -
590B ILE* 3.0 26.0 + - - +
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Residues in contact with THR 563 (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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445A SER* 4.4 11.7 + - - +
447A PRO* 5.6 0.7 - - - +
437B VAL* 2.8 26.1 + - - +
438B PHE* 3.8 19.9 - - - -
441B SER* 4.8 0.2 - - - -
560B GLU* 3.4 8.8 - - - +
562B ASN* 1.3 100.7 + - - +
564B VAL* 1.3 64.8 + - - +
565B VAL* 2.9 41.1 - - + +
567B GLY* 4.2 1.4 - - - -
590B ILE* 3.3 6.3 - - - +
591B PRO 3.7 15.4 + - - -
592B ASP* 4.5 5.0 + - - +
593B GLU 5.2 0.3 + - - -
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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