Contacts of the helix formed by residues 603 - 606 (chain B) 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 PRO 603 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522B LEU* 3.8 14.5 - - + +
523B ASN* 3.7 42.1 + - - +
526B CYS* 3.8 22.4 - - + -
599B LEU 3.3 16.4 - - - +
600B LYS* 4.1 5.6 - - - +
601B THR 3.6 3.1 - - - -
602B LEU* 1.3 94.8 - - + +
604B GLN* 1.3 63.0 + - + +
605B MET 3.7 0.2 + - - -
606B PHE* 4.3 4.9 + - - +
607B THR* 4.2 9.2 + - - +
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Residues in contact with GLN 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLU* 4.5 11.2 - - - +
600B LYS 3.4 23.8 + - - +
601B THR* 3.5 18.4 + - + +
602B LEU 3.0 1.0 - - - -
603B PRO* 1.3 79.4 - - + +
605B MET* 1.3 61.0 + - - +
606B PHE 3.4 1.6 - - - -
607B THR* 3.3 18.9 + - - +
608B LYS* 6.1 1.4 - - - -
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Residues in contact with MET 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLU* 5.5 3.1 - - - -
183A ILE* 3.9 27.6 - - + -
185A LYS* 5.9 0.7 + - - -
556B TYR* 3.9 24.5 - - - -
567B MET* 5.0 3.4 - - - +
598B LEU* 3.6 21.3 - - + -
601B THR* 3.3 29.4 - - + +
602B LEU* 3.0 35.8 + - + +
604B GLN* 1.3 77.3 - - - +
606B PHE* 1.3 83.6 + - + +
607B THR 3.9 0.2 - - - -
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Residues in contact with PHE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 5.8 2.5 - - - -
512B VAL* 3.7 41.1 - - + +
517B VAL* 3.5 22.8 - - + +
522B LEU* 4.5 5.4 - - + -
548B THR* 3.9 7.0 - - - -
550B ASP* 5.3 1.8 - - - -
554B HIS* 4.2 4.7 - + - -
556B TYR* 3.2 22.2 - - - -
567B MET* 4.1 20.0 - - + -
602B LEU* 3.6 26.0 - - + -
603B PRO 4.3 3.4 + - - +
604B GLN 3.4 0.4 - - - -
605B MET* 1.3 104.4 - - + +
607B THR* 1.3 66.2 + - - +
608B LYS 3.1 3.6 - - - -
609B THR* 2.6 37.0 + - + +
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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