Contacts of the strand formed by residues 543 - 557 (chain B) in PDB entry 2W77
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 543 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539B VAL* 3.0 47.9 + - + -
540B THR* 3.1 26.4 + - - +
541B ASP 3.7 0.8 - - - -
542B ASP* 1.3 80.6 - - - +
544B ASN* 1.3 74.5 + - - +
545B LEU* 5.5 8.3 - - + -
575B ALA* 4.5 12.6 - - + -
576B VAL 3.9 10.1 - - - +
577B TYR* 4.2 24.7 - - + -
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Residues in contact with ASN 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B ARG* 3.1 49.7 + - + +
537B PHE 3.2 13.3 - - - +
538B ASN* 3.6 23.0 + - - +
540B THR 4.6 1.0 + - - -
541B ASP 5.2 3.2 + - - -
542B ASP 4.5 2.6 - - - -
543B LEU* 1.3 88.8 + - - +
545B LEU* 1.3 59.6 + - - +
546B PHE* 4.1 2.4 + - + -
575B ALA* 3.3 4.7 - - - +
576B VAL* 2.9 46.0 + - + +
578B ASP* 5.5 3.8 + - - -
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Residues in contact with LEU 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ALA 3.5 2.4 - - - +
536B ARG* 4.6 0.4 - - - -
537B PHE* 2.9 46.0 + - + +
539B VAL* 4.2 20.9 - - + +
543B LEU* 4.3 8.7 - - + -
544B ASN* 1.3 71.0 - - - +
546B PHE* 1.3 63.5 + - - +
547B LEU* 3.7 39.0 - - + -
573B VAL* 6.0 2.5 - - + -
574B GLY 3.8 4.9 - - - +
575B ALA* 4.4 15.7 - - + +
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Residues in contact with PHE 546 (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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156B THR* 4.4 13.5 - - + -
158B LEU* 4.7 4.0 - - + -
160B LEU* 3.6 17.5 - - + -
164B GLU 3.5 13.7 - - - -
166B PRO* 3.8 18.2 - - + -
534B THR* 4.8 4.7 - - + -
535B ALA 3.3 6.5 - - - +
536B ARG* 3.3 49.8 - - + -
544B ASN* 4.3 5.8 - - + -
545B LEU* 1.3 75.0 - - - +
547B LEU* 1.3 64.6 + - - +
572B TYR* 3.9 28.5 - + + -
573B VAL* 3.3 4.9 - - - +
574B GLY 2.6 41.3 + - - +
576B VAL* 3.7 26.0 - - + -
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Residues in contact with LEU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B THR* 4.6 2.2 - - - -
535B ALA* 2.9 33.2 + - - +
537B PHE* 4.6 17.3 - - + -
545B LEU* 3.7 29.1 + - + -
546B PHE* 1.3 81.7 - - - +
548B GLY* 1.3 57.8 + - - +
572B TYR* 3.4 2.2 - - - -
573B VAL* 3.8 30.7 - - + -
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Residues in contact with GLY 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B MET* 3.1 17.7 - - - -
534B THR* 3.9 6.7 - - - -
547B LEU* 1.3 76.4 - - - +
549B GLY* 1.3 59.0 + - - -
569B PHE* 4.4 5.7 - - - -
571B PRO* 3.8 3.1 - - - +
572B TYR* 2.8 34.5 + - - +
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Residues in contact with GLY 549 (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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255B LEU* 4.0 15.6 - - - +
531B SER 3.7 0.5 - - - +
532B TYR* 3.1 22.2 - - - -
533B MET* 2.9 20.8 + - - +
548B GLY* 1.3 75.9 - - - -
550B ARG* 1.3 62.9 + - - -
569B PHE* 4.3 11.7 - - - -
570B ILE 3.1 12.8 - - - -
572B TYR 4.4 1.6 - - - -
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Residues in contact with ARG 550 (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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254B GLY 3.5 11.9 - - - +
255B LEU* 2.6 42.8 + - - +
256B LEU* 3.7 15.0 + - - +
257B THR 4.9 0.8 + - - -
258B GLY* 3.5 20.6 - - - +
458B ASP* 5.4 0.4 + - - -
479B SER* 3.2 28.7 + - - -
528B GLN* 4.6 5.9 + - - -
530B GLY* 3.7 14.2 - - - +
531B SER 3.1 15.5 - - - +
532B TYR* 3.6 20.5 - - + -
549B GLY* 1.3 75.5 - - - +
551B VAL* 1.3 66.0 + - - +
552B VAL* 3.6 20.5 + - + +
568B ARG 3.4 3.1 - - - +
569B PHE* 3.4 4.4 - - - -
570B ILE* 2.8 47.0 + - + +
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Residues in contact with VAL 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B LEU 3.9 0.7 - - - +
530B GLY* 3.5 6.2 - - - -
531B SER* 2.8 46.9 + - - +
533B MET* 5.4 9.6 - - + -
550B ARG* 1.3 74.9 - - - +
552B VAL* 1.3 60.9 + - - +
567B GLY* 4.9 15.9 - - - +
568B ARG 3.4 7.0 - - - +
569B PHE* 4.3 17.5 - - + -
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Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLY* 4.4 4.5 - - - -
259B ALA* 4.8 4.5 - - + +
528B GLN* 4.0 16.6 - - - +
529B LEU 3.7 4.0 - - - +
550B ARG* 3.6 33.2 - - + +
551B VAL* 1.3 80.4 - - - +
553B ASP* 1.3 70.7 + - - +
554B TYR* 4.7 4.7 - - + +
565B GLU 3.7 3.6 - - - +
567B GLY* 3.2 8.5 + - - -
568B ARG* 2.9 31.9 + - - +
570B ILE* 3.7 19.1 - - + -
593B PHE* 3.5 26.6 - - + -
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Residues in contact with ASP 553 (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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527B ARG* 4.3 4.9 + - - -
528B GLN* 3.2 8.3 - - - +
529B LEU* 3.0 56.6 + - + +
551B VAL 4.3 0.2 + - - -
552B VAL* 1.3 75.5 - - - +
554B TYR* 1.3 76.8 + - - +
555B ARG 4.4 0.7 + - - -
564B ARG* 3.0 28.3 + - - -
565B GLU 3.4 2.0 - - - -
566B SER* 2.5 28.3 + - - -
567B GLY 4.4 2.5 + - - +
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Residues in contact with TYR 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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227B ARG* 4.9 8.0 - - - -
259B ALA* 3.9 17.3 - - + -
526B THR* 3.6 30.4 + - + +
527B ARG 3.4 3.8 - - - -
528B GLN* 3.9 31.9 - - + -
552B VAL* 4.7 7.0 - - + -
553B ASP* 1.3 77.2 + - - +
555B ARG* 1.3 58.5 + - - +
556B VAL* 3.5 28.5 - - + +
563B ILE* 3.8 1.7 - - + +
564B ARG* 3.4 5.2 + - - -
565B GLU* 2.9 47.0 + - + +
593B PHE* 5.3 0.9 - - + -
594B MET* 4.2 19.0 - - - +
595B PRO* 3.5 32.5 - - + -
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Residues in contact with ARG 555 (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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525B LYS 4.4 0.7 - - - -
526B THR* 3.5 2.3 - - - +
527B ARG* 2.6 74.8 + - + +
553B ASP* 4.4 0.4 + - - -
554B TYR* 1.3 74.1 - - - +
556B VAL* 1.3 64.8 + - - +
557B THR* 4.1 25.4 - - + +
562B THR* 4.5 12.2 + - + +
563B ILE 3.6 3.8 - - - +
564B ARG* 3.4 44.6 - - + +
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Residues in contact with VAL 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B ASP* 4.7 14.1 - - + +
525B LYS 3.2 10.5 - - - +
526B THR* 3.8 21.8 - - - +
554B TYR* 3.5 28.9 - - + +
555B ARG* 1.3 75.0 - - - +
557B THR* 1.3 66.1 + - - +
558B GLY 4.2 0.2 + - - -
560B ASN 5.5 0.2 - - - +
561B PRO 4.8 0.7 - - - +
562B THR* 3.9 1.8 - - - -
563B ILE* 3.2 57.4 + - + +
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Residues in contact with THR 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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523B ASP 4.4 0.2 - - - +
524B ASP* 3.6 4.0 - - - +
525B LYS* 2.9 48.8 + - - +
555B ARG* 4.1 30.5 - - + +
556B VAL* 1.3 76.8 - - - +
558B GLY* 1.3 58.1 + - - +
562B THR* 3.7 23.8 - - - +
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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