Contacts of the helix formed by residues 519 - 530 (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 SER 519 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B LYS* 4.1 3.1 - - - +
495E ASP* 2.4 35.3 + - - -
517E SER 3.5 3.2 + - - -
518E VAL* 1.3 72.5 - - - +
520E PHE* 1.3 64.2 + - - +
521E GLY* 3.7 1.5 + - - -
522E ALA* 3.0 24.9 + - - +
523E CYS* 3.2 11.4 + - - -
549E GLU 3.3 16.4 - - - -
550E SER* 3.6 18.6 - - - -
551E CYS 3.7 7.0 - - - -
552E PRO* 4.1 2.7 - - - +
553E VAL* 4.5 0.7 - - - -
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Residues in contact with PHE 520 (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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518E VAL 3.7 1.2 + - - -
519E SER* 1.3 70.8 - - - +
521E GLY* 1.3 63.6 + - - +
523E CYS* 3.3 3.5 + - - +
524E LYS* 2.9 40.4 + - + +
537E VAL* 4.4 9.6 - - + -
544E PRO* 3.7 40.8 - - + +
545E ASP* 4.0 23.6 - - - -
547E ARG 5.5 0.4 - - - -
548E PRO 5.0 1.6 - - - +
549E GLU* 3.5 34.3 + - - +
551E CYS 3.3 13.3 + - - +
553E VAL* 3.7 19.6 - - + +
576E MET* 3.7 33.7 - - + -
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Residues in contact with GLY 521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LYS* 3.7 17.3 - - - -
519E SER* 3.0 2.8 - - - -
520E PHE* 1.3 71.5 - - - +
522E ALA* 1.3 62.0 + - - +
524E LYS* 3.1 12.7 + - - +
525E LEU* 3.2 12.0 + - - +
549E GLU* 2.8 48.5 + - - +
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Residues in contact with ALA 522 (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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496B LYS* 3.6 13.4 - - + +
495E ASP* 3.5 24.0 - - + +
498E LEU* 4.8 3.8 - - + -
499E LEU* 3.9 16.8 - - + +
518E VAL* 4.5 6.5 - - + -
519E SER* 3.0 21.6 + - - +
521E GLY* 1.3 73.6 - - - +
523E CYS* 1.3 66.9 + - - +
525E LEU* 4.0 1.0 - - - +
526E LEU* 3.0 26.2 + - - +
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Residues in contact with CYS 523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498E LEU* 5.6 1.8 - - - -
518E VAL* 3.9 13.4 - - - +
519E SER 3.2 12.7 + - - -
520E PHE 3.5 8.1 - - - +
522E ALA* 1.3 75.8 - - - +
524E LYS* 1.3 62.3 + - - +
526E LEU* 4.6 2.0 - - - -
527E GLY 3.2 16.3 + - - -
535E VAL* 3.9 8.7 - - + +
537E VAL* 3.6 33.7 - - + -
553E VAL* 4.3 10.5 - - - -
556E VAL* 3.7 23.8 - - - -
576E MET* 3.3 19.6 - - + +
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Residues in contact with LYS 524 (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* 2.9 47.7 + - + +
521E GLY 3.4 7.2 - - - +
522E ALA 3.0 0.8 - - - -
523E CYS* 1.3 79.4 - - - +
525E LEU* 1.4 61.9 + - - +
527E GLY* 3.3 9.0 + - - -
528E GLN* 3.3 12.9 + - - +
545E ASP* 5.6 1.6 + - - -
549E GLU* 2.7 39.0 + - - -
576E MET* 4.3 13.4 - - - +
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Residues in contact with LEU 525 (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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470B ASP* 4.9 5.6 - - + -
471B LEU* 3.8 40.2 - - + +
474B HIS* 4.3 19.5 - - + +
496B LYS* 3.7 38.6 - - + +
497B ALA* 4.0 11.0 - - + +
500B ALA* 4.3 12.6 - - + -
499E LEU* 4.5 7.0 - - + -
521E GLY 3.2 9.4 + - - +
522E ALA* 4.0 6.1 - - - +
524E LYS* 1.4 74.2 - - - +
526E LEU* 1.3 57.8 + - - +
528E GLN* 2.8 7.4 + - + +
529E LYS* 2.7 36.1 + - - +
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Residues in contact with LEU 526 (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* 4.2 15.7 - - + +
499E LEU* 3.9 17.4 - - + +
502E ALA* 3.6 33.2 - - + -
505E LEU* 4.0 15.3 - - + -
522E ALA 3.0 16.3 + - - +
523E CYS* 4.0 4.7 - - - +
525E LEU* 1.3 78.1 - - - +
527E GLY* 1.3 52.5 + - - +
529E LYS* 3.1 5.1 + - + +
530E MET* 2.9 45.2 + - + +
533E LEU* 4.9 0.4 - - + -
535E VAL* 4.1 16.4 - - + -
558E ILE* 3.8 30.3 - - + -
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Residues in contact with GLY 527 (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 3.2 11.4 + - - -
524E LYS 3.5 3.4 - - - -
525E LEU 3.2 0.2 - - - -
526E LEU* 1.3 76.7 - - - +
528E GLN* 1.3 61.2 + - - +
530E MET 3.7 8.2 + - - -
531E PRO* 3.8 14.0 - - - +
533E LEU 5.4 1.5 - - - +
535E VAL* 4.1 11.9 - - - +
576E MET* 3.4 31.3 - - - +
577E ASP* 4.8 5.8 - - - +
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Residues in contact with GLN 528 (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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471B LEU* 4.2 19.4 - - + +
474B HIS* 4.6 11.6 + - - +
475B HIS* 3.9 20.9 + - - -
524E LYS 3.3 10.6 + - - +
525E LEU* 2.8 21.1 + - + +
527E GLY* 1.3 72.5 - - - +
529E LYS* 1.4 68.2 + - - +
530E MET 3.5 0.2 + - - -
531E PRO* 3.7 8.0 - - - +
576E MET 4.4 1.3 + - - +
577E ASP 4.4 2.1 + - - +
578E GLN* 3.0 42.3 + - + +
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Residues in contact with LYS 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B HIS* 4.1 20.8 + - + -
478B SER* 5.9 0.8 - - - -
500B ALA* 2.8 40.3 + - + +
501B ASN* 3.8 15.8 - - - +
499E LEU* 6.0 0.2 - - + -
502E ALA* 4.0 17.0 - - + -
503E SER* 5.3 6.7 - - - +
525E LEU* 2.7 13.4 + - + +
526E LEU* 3.8 9.4 - - + +
528E GLN* 1.4 78.4 - - - +
530E MET* 1.3 93.6 + - + +
531E PRO* 2.9 12.1 - - - +
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Residues in contact with MET 530 (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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502E ALA* 4.1 21.1 - - + +
503E SER* 4.3 9.9 - - - +
506E GLU* 4.7 17.7 - - - +
526E LEU* 2.9 30.9 + - + +
527E GLY* 3.8 6.3 - - - +
528E GLN 3.3 0.6 - - - -
529E LYS* 1.3 128.5 - - + +
531E PRO* 1.3 69.5 - - - +
532E LYS 2.7 5.0 + - - +
533E LEU* 2.9 48.3 + - + +
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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