Contacts of the strand formed by residues 485 - 489 (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 LYS 485 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E HIS* 6.5 0.4 - - + -
459E GLU 2.9 6.1 + - - +
460E MET* 3.3 36.3 - - + +
461E LEU 3.2 25.1 + - - +
483E LEU* 3.5 5.3 - - - +
484E ARG* 1.3 92.6 - - + +
486E LEU* 1.3 59.4 + - - +
487E GLU* 4.2 4.5 - - + +
509E ARG* 3.8 30.7 - - + +
510E SER* 3.7 13.2 - - - +
601E IHP 2.4 70.0 + - - +
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Residues in contact with LEU 486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461E LEU* 3.3 36.1 - - + +
462E SER* 5.6 0.2 - - - -
463E VAL* 5.7 0.4 - - + -
473E MET* 4.7 5.2 - - + -
476E VAL* 4.1 11.4 - - + -
477E LEU* 3.9 19.1 - - + -
483E LEU* 3.9 18.8 - - + -
485E LYS* 1.3 71.0 - - - +
487E GLU* 1.3 63.9 + - - +
488E ILE* 3.7 33.0 - - + -
508E MET* 3.6 17.6 - - + +
510E SER* 3.3 7.6 + - - +
511E LEU* 3.3 13.9 - - + -
512E TRP* 2.7 31.9 + - - +
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Residues in contact with GLU 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E PRO* 5.8 0.7 - - - +
78E HIS* 2.5 48.0 + - - +
79E PHE* 3.2 28.3 + - + -
436E ARG* 5.0 0.5 + - - -
460E MET* 5.0 9.3 - - + +
461E LEU 3.0 10.9 + - - +
462E SER* 2.5 26.7 + - - +
463E VAL 2.9 26.5 + - - +
485E LYS* 5.5 4.5 - - + +
486E LEU* 1.3 76.8 - - - +
488E ILE* 1.3 61.0 - - - +
512E TRP* 3.4 16.2 - - + -
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Residues in contact with ILE 488 (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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79E PHE* 4.0 4.0 - - - -
448E PHE* 6.3 0.2 - - + -
463E VAL* 3.3 13.7 - - + -
473E MET* 4.0 22.0 - - + -
486E LEU* 3.7 36.3 - - + -
487E GLU* 1.3 78.8 - - - +
489E ARG* 1.3 63.1 + - - +
491E CYS* 3.6 34.5 - - + -
493E PHE* 3.8 15.9 - - + -
512E TRP* 2.9 13.5 + - - +
513E MET* 3.3 12.8 - - + -
514E SER 2.9 24.9 + - - -
516E CYS* 4.0 8.4 - - - -
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Residues in contact with ARG 489 (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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79E PHE* 4.1 15.5 - - + -
82E PHE* 5.4 0.6 - - - +
84E LEU* 3.9 21.2 - - + +
463E VAL 2.9 11.5 + - - +
464E ALA* 3.2 26.8 - - + -
465E PHE* 3.1 25.7 + - - -
488E ILE* 1.3 73.6 - - - +
490E ASP* 1.3 108.5 + - - +
491E CYS* 3.2 7.5 - - - -
514E SER* 3.3 21.1 - - - +
516E CYS* 4.3 0.4 - - - -
602E CFA 4.4 3.1 - - + -
2F VAL* 3.6 18.6 - - - +
3F VAL* 2.5 30.3 + - - +
4F GLY* 3.0 26.3 + - - -
5F TRP* 3.4 10.8 - - - +
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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
------------------------------------------------------------
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