Contacts of the strand formed by residues 555 - 560 (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 ARG 555 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83E ASN 5.8 0.6 + - - -
84E LEU* 2.9 26.0 + - - +
86E PRO* 3.4 31.0 - - - +
512E TRP* 3.9 24.7 - - + -
513E MET 3.3 11.2 - - - +
514E SER* 4.0 7.4 - - - -
536E GLU 4.5 0.2 - - - -
537E VAL* 3.6 3.5 - - - -
538E ILE* 2.8 75.8 + - + +
539E ASP* 4.0 1.0 - - - +
540E GLU* 3.8 10.7 + - - +
553E VAL* 3.7 7.6 - - - +
554E GLU* 1.3 114.5 + - - +
556E VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 556 (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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498E LEU* 5.8 1.1 - - + -
511E LEU 3.9 1.9 - - - +
512E TRP* 3.7 2.9 - - - -
513E MET* 2.9 51.9 + - + +
518E VAL* 4.2 20.2 - - + -
523E CYS* 3.7 23.1 - - - -
535E VAL* 4.1 11.4 - - + -
536E GLU 3.5 9.2 - - - +
537E VAL 4.9 0.2 - - - +
553E VAL* 4.0 13.7 - - + -
555E ARG* 1.3 76.9 - - - +
557E PHE* 1.3 60.5 + - - +
558E ILE* 3.8 28.2 - - + +
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Residues in contact with PHE 557 (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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52E ASN* 5.4 7.6 - - - -
77E PRO* 3.8 28.7 - - + -
89E TRP* 3.7 31.6 - + - -
510E SER* 3.5 29.2 - - - -
511E LEU 3.7 6.7 - - - -
512E TRP* 3.6 28.7 - + + -
534E ASN 3.5 1.7 - - - +
536E GLU* 2.7 48.8 + - + +
538E ILE* 4.1 11.0 - - + +
556E VAL* 1.3 74.1 - - - +
558E ILE* 1.3 58.4 + - - +
559E TYR* 3.4 36.8 - + + -
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Residues in contact with ILE 558 (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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498E LEU* 4.0 21.3 - - + -
505E LEU* 4.3 12.3 - - + -
510E SER* 3.1 5.9 - - - -
511E LEU* 2.9 49.5 + - + +
513E MET* 5.8 0.7 - - - -
526E LEU* 3.8 20.4 - - + -
533E LEU* 4.1 32.8 - - + -
534E ASN 3.4 4.5 - - - -
535E VAL* 4.2 14.1 - - + -
556E VAL* 3.8 26.7 - - + +
557E PHE* 1.3 78.0 - - - +
559E TYR* 1.3 63.9 + - - +
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Residues in contact with TYR 559 (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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52E ASN* 3.3 20.6 - - - +
54E TYR* 3.6 28.8 - + + +
89E TRP* 4.9 2.7 - + - -
505E LEU 5.8 0.7 - - - -
509E ARG 3.4 17.7 - - - +
510E SER* 3.9 6.7 - - - +
533E LEU* 4.2 4.0 - - - -
534E ASN* 3.2 56.3 + - + -
536E GLU* 2.6 39.0 + - + -
557E PHE* 3.4 34.8 - + + -
558E ILE* 1.3 77.6 - - - +
560E ARG* 1.3 68.3 + - - +
561E THR* 4.1 2.5 - - + -
566E ARG* 3.5 14.0 - - - -
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Residues in contact with ARG 560 (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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156D GLN* 3.6 26.5 + - - +
157D TRP* 3.4 55.1 + - + +
160D GLU* 5.4 1.0 + - - -
52E ASN* 4.5 0.9 - - - +
55E ALA* 4.2 9.1 - - + +
505E LEU 4.5 3.2 + - - +
506E GLU* 2.8 35.6 + - - +
507E THR* 3.2 20.6 + - - +
508E MET 3.2 29.6 + - - +
509E ARG* 3.8 11.3 + - - +
532E LYS 3.4 7.9 - - - -
533E LEU* 3.5 17.2 - - + +
559E TYR* 1.3 80.8 - - - +
561E THR* 1.3 61.5 + - - +
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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