Contacts of the strand formed by residues 542 - 552 (chain A) in PDB entry 2P2B
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 ILE 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536A LEU* 3.3 43.3 - - + +
537A VAL* 3.3 23.2 - - + +
539A HIS* 2.9 21.6 + - + +
540A PRO 3.5 0.2 - - - -
541A LYS* 1.3 81.9 - - + +
543A ALA* 1.3 63.3 + - - +
544A GLU 3.7 24.2 - - - +
563A VAL* 3.8 25.6 - - + -
564A THR 3.7 4.9 - - - +
565A LEU* 4.3 8.3 - - + -
566A ASN* 3.9 6.2 + - - +
579A VAL* 3.9 28.5 - - + -
582A TRP* 5.6 0.7 - - + -
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Residues in contact with ALA 543 (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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537A VAL* 3.7 17.6 - - - +
541A LYS 3.9 0.8 + - - -
542A ILE* 1.3 74.1 - - - +
544A GLU* 1.3 66.3 + - + +
564A THR* 2.9 14.4 + - + +
565A LEU 4.2 0.7 - - - -
566A ASN* 3.2 23.2 + - - +
64B ASN* 3.2 35.4 - - + +
66B SER* 5.6 6.1 - - - -
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Residues in contact with GLU 544 (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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537A VAL* 3.8 8.5 - - + -
542A ILE* 3.7 3.5 - - - +
543A ALA* 1.3 84.6 - - + +
545A ALA* 1.3 65.9 + - - +
563A VAL* 3.5 0.7 - - - -
564A THR* 2.6 45.3 + - + +
602A LEU* 3.6 22.7 - - + +
604A LYS* 3.0 42.5 + - - -
610A ILE* 5.1 6.8 - - - +
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Residues in contact with ALA 545 (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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533A GLU* 3.6 21.1 - - - +
536A LEU* 3.6 41.1 - - + -
537A VAL* 3.7 10.7 - - + +
542A ILE* 4.7 1.3 - - + -
544A GLU* 1.3 82.0 - - - +
546A ALA* 1.3 60.6 + - - +
562A TYR 3.1 11.9 - - - +
563A VAL* 4.5 4.5 - - + -
602A LEU* 4.4 5.5 - - - +
610A ILE* 5.3 4.3 - - - +
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Residues in contact with ALA 546 (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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533A GLU* 3.3 7.4 - - - +
545A ALA* 1.3 74.7 - - - +
547A VAL* 1.3 62.0 + - - +
561A ALA* 3.7 0.2 - - - -
562A TYR* 2.9 37.5 + - - -
602A LEU* 3.8 13.9 - - + +
610A ILE* 3.8 16.4 - - + -
612A ARG* 4.8 2.7 - - + -
615A LEU* 3.4 32.3 - - + -
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Residues in contact with VAL 547 (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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520A LEU* 4.1 14.6 - - + -
529A THR* 3.6 24.7 - - - +
532A ILE* 3.8 20.2 - - + -
533A GLU* 2.8 27.8 + - + +
536A LEU* 3.7 30.7 - - + -
546A ALA* 1.3 75.0 - - - +
548A VAL* 1.3 71.3 + - - +
559A ILE* 3.8 26.0 - - + -
560A TYR 3.5 3.6 - - - +
561A ALA* 3.9 9.2 - - + -
612A ARG* 3.8 6.3 - - - +
616A ARG* 5.5 0.2 + - - -
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Residues in contact with VAL 548 (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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520A LEU* 4.1 8.0 - - - +
529A THR* 4.9 0.7 - - - -
547A VAL* 1.3 82.2 - - - +
549A GLY* 1.3 65.2 + - - +
559A ILE* 3.9 3.1 - - - -
560A TYR* 2.9 42.8 + - + +
562A TYR* 3.9 10.5 - - + -
612A ARG* 4.0 20.0 - - + +
615A LEU* 4.1 11.0 - - + +
616A ARG* 3.8 36.8 - - + +
619A ALA* 3.8 29.6 - - + -
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Residues in contact with GLY 549 (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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520A LEU* 3.4 26.8 - - - +
548A VAL* 1.3 80.8 - - - +
550A ILE* 1.3 66.2 + - - +
551A PRO* 4.7 1.2 - - - +
557A GLN* 3.8 17.8 + - - +
558A ALA 3.4 8.7 - - - -
616A ARG* 4.3 16.3 - - - +
620A ALA* 5.8 0.5 - - - +
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Residues in contact with ILE 550 (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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548A VAL* 4.7 0.2 - - + -
549A GLY* 1.3 78.3 - - - +
551A PRO* 1.3 76.6 - - + +
557A GLN* 3.1 8.3 - - - -
558A ALA* 2.8 56.0 + - + +
559A ILE 5.7 0.2 - - - -
560A TYR* 4.0 25.6 - - + -
595A VAL* 4.7 10.5 - - + -
616A ARG 4.9 0.2 - - - +
619A ALA* 3.5 46.7 - - + +
620A ALA* 3.8 5.8 - - + +
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Residues in contact with PRO 551 (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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549A GLY 4.7 1.3 - - - +
550A ILE* 1.3 98.7 - - + +
552A HIS* 1.3 59.8 + - - +
556A GLY 3.5 8.5 - - - +
557A GLN* 5.0 1.7 - - + +
620A ALA* 4.2 20.4 - - + +
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Residues in contact with HIS 552 (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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362A ARG* 5.5 0.2 - - - -
551A PRO* 1.3 77.6 + - - +
553A ALA* 1.3 62.5 + - + +
554A ILE* 3.3 22.9 + - - +
555A LYS* 3.1 53.8 - - + +
556A GLY* 3.0 30.8 + - - +
557A GLN 4.1 4.0 - - - -
558A ALA* 3.8 31.4 - - + +
990A COA 6.2 0.6 - - - +
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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