Contacts of the strand formed by residues 533 - 538 (chain E) in PDB entry 2P1N
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 533 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502E ALA 4.5 0.4 - - - +
505E LEU* 3.9 28.7 - - + +
506E GLU* 4.2 20.0 - - + +
526E LEU* 4.9 3.8 - - + -
527E GLY* 5.4 1.9 - - - +
530E MET* 2.9 50.1 + - + +
531E PRO* 3.4 8.4 - - - +
532E LYS* 1.3 78.7 - - - +
534E ASN* 1.3 60.6 - - - +
535E VAL* 4.0 17.9 + - + +
558E ILE* 4.1 16.4 - - + -
559E TYR 3.6 4.7 - - - +
560E ARG* 3.5 31.6 - - + +
575E ASN* 5.7 0.9 + - - -
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Residues in contact with ASN 534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TYR 4.7 1.0 + - - -
531E PRO 5.3 1.4 - - - +
533E LEU* 1.3 71.9 - - - +
535E VAL* 1.3 60.8 + - - +
536E GLU* 3.5 3.1 + - + +
557E PHE 3.5 2.8 - - - +
558E ILE* 3.4 4.9 - - - -
559E TYR* 3.2 71.4 + - + +
561E THR* 3.4 12.1 + - - +
564E GLY* 3.1 23.6 + - - -
565E PRO* 3.3 26.1 - - - +
566E ARG* 4.1 3.4 - - - +
575E ASN* 3.5 20.2 + - - +
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Residues in contact with VAL 535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523E CYS* 3.9 16.2 - - + +
526E LEU* 4.1 23.1 - - + +
527E GLY* 4.1 18.4 - - - +
533E LEU* 3.8 20.3 + - + +
534E ASN* 1.3 72.5 - - - +
536E GLU* 1.3 58.3 + - - +
556E VAL* 4.1 20.2 - - + -
557E PHE 4.0 2.7 - - - -
558E ILE* 4.2 9.0 - - + -
575E ASN* 3.9 4.9 + - - +
576E MET* 3.1 47.1 + - + +
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Residues in contact with GLU 536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E TRP* 3.3 16.8 + - - -
534E ASN* 4.2 4.0 + - - +
535E VAL* 1.3 70.9 - - - +
537E VAL* 1.4 60.1 + - - +
538E ILE* 3.4 12.1 - - + +
556E VAL* 3.5 3.5 - - - -
557E PHE* 2.7 45.7 + - + +
559E TYR* 2.6 30.8 + - + +
566E ARG* 2.6 49.8 + - - +
569E MET* 4.3 9.6 - - + +
573E VAL* 4.0 13.4 - - + +
574E TRP 3.6 4.9 - - - -
575E ASN* 4.4 9.6 - - - +
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Residues in contact with VAL 537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520E PHE* 4.4 4.3 - - + -
523E CYS* 3.6 39.5 - - + -
535E VAL 3.7 0.6 + - - -
536E GLU* 1.4 71.4 - - - +
538E ILE* 1.3 61.0 + - - +
539E ASP* 4.1 14.4 - - + -
544E PRO* 4.5 16.2 - - + -
553E VAL* 3.7 28.7 - - + -
555E ARG 3.6 4.7 - - - -
556E VAL* 4.7 0.7 - - - +
572E PHE 3.8 0.5 - - - +
573E VAL* 3.3 4.7 - - - -
574E TRP* 3.0 39.9 + - + +
576E MET* 4.0 18.6 - - + -
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Residues in contact with ILE 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E VAL* 5.5 0.4 - - + -
86E PRO* 4.1 18.2 - - + -
89E TRP* 3.4 31.4 - - + +
512E TRP* 4.0 26.7 - - + -
536E GLU* 3.4 20.0 - - + +
537E VAL* 1.3 75.9 - - - +
539E ASP* 1.3 58.5 + - - +
555E ARG* 2.8 51.3 + - + +
557E PHE* 4.1 12.3 - - + +
572E PHE* 3.4 28.3 - - + -
573E VAL* 4.1 7.9 - - + -
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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