Contacts of the strand formed by residues 564 - 569 (chain A) in PDB entry 2NUP
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 ASP 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A HIS* 2.9 26.4 + - + +
562A LYS 2.7 9.2 + - - +
563A ASP* 1.3 77.1 - - - +
565A PRO* 1.3 62.9 - - - +
566A SER* 3.5 17.7 + - - -
567A SER* 2.5 49.9 + - - -
761A VAL* 3.3 7.1 - - - +
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Residues in contact with PRO 565 (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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563A ASP 3.6 6.3 - - - +
564A ASP* 1.3 86.7 - - - +
566A SER* 1.3 64.8 + - - +
568A PHE* 3.0 22.9 + - - +
754A ASP* 5.3 4.9 - - - +
757A LYS* 3.9 27.9 - - + +
758A LYS* 3.9 25.8 - - + +
761A VAL* 3.4 22.6 - - + -
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Residues in contact with SER 566 (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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564A ASP* 3.2 11.7 + - - -
565A PRO* 1.3 78.2 - - - +
567A SER* 1.3 60.5 + - - +
568A PHE 3.4 6.1 + - - +
569A ARG* 5.5 0.7 - - - +
757A LYS* 5.3 7.0 + - - +
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Residues in contact with SER 567 (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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559A GLU 3.5 2.6 - - - +
560A TYR* 3.1 4.7 - - - +
561A HIS* 2.7 41.4 + - - -
564A ASP* 2.5 38.8 + - - -
566A SER* 1.3 78.4 - - - +
568A PHE* 1.3 60.3 + - - +
569A ARG* 2.9 33.7 + - - +
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Residues in contact with PHE 568 (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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554A CYS* 3.1 55.4 - - + -
555A GLN* 5.3 0.2 - - - -
558A GLY* 3.7 8.1 - - - -
559A GLU 2.9 16.8 - - - -
560A TYR* 4.0 13.2 - + + -
565A PRO 3.0 15.0 + - - +
566A SER 4.0 5.2 - - - +
567A SER* 1.3 80.0 + - - +
569A ARG* 1.3 73.6 + - - +
570A PHE* 3.9 24.7 - + + -
578A PRO* 5.9 1.6 - - + -
753A MET* 5.9 4.9 - - + -
756A LEU* 5.6 4.0 - - + -
757A LYS* 4.3 35.4 + - + -
760A ALA* 3.9 17.5 - - + -
761A VAL* 4.5 4.9 - - + -
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Residues in contact with ARG 569 (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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558A GLY* 3.7 4.3 - - - -
559A GLU* 3.0 61.8 + - + +
560A TYR* 4.2 11.7 + - - +
561A HIS* 5.0 12.3 + - - -
566A SER 5.5 0.7 - - - +
567A SER* 2.9 23.5 + - - +
568A PHE* 1.3 82.9 - - - +
570A PHE* 1.3 65.0 + - - +
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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