Contacts of the strand formed by residues 185 - 190 (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 LYS 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A HIS* 3.8 6.2 + - - +
177A GLU* 3.0 74.6 + - + +
180A CYS* 3.4 23.7 - - + +
183A ILE* 4.3 2.4 - - + +
184A SER* 1.3 72.8 - - - +
186A SER* 1.3 63.3 + - - +
187A TYR* 5.1 2.9 + - + -
567B MET* 3.3 61.1 - - + +
569B ILE* 4.0 12.4 - - + +
605B MET 5.9 0.8 + - - -
606B PHE* 5.8 2.2 - - - -
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Residues in contact with SER 186 (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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174A GLN* 2.9 28.9 + - - +
175A VAL 3.3 14.6 - - - -
176A HIS* 3.7 23.7 - - - -
177A GLU 4.3 0.7 - - - +
185A LYS* 1.3 76.6 - - - +
187A TYR* 1.3 66.7 + - - +
188A VAL* 3.9 0.9 + - - +
567B MET 3.3 3.9 + - - +
568B LEU* 3.8 13.7 - - - +
569B ILE* 3.0 24.9 + - - +
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL 3.3 5.0 - - - +
174A GLN* 3.4 1.2 - - - -
175A VAL* 2.8 33.4 + - + +
177A GLU* 3.8 15.4 + - + -
185A LYS* 5.1 2.6 + - + -
186A SER* 1.3 76.2 - - - +
188A VAL* 1.3 61.1 + - - +
189A PHE* 3.4 20.5 - - + -
203A MET 4.0 14.8 - - - -
204A LEU* 3.3 24.4 + - + -
228A ARG* 3.1 20.8 + - - -
229A PHE* 3.6 28.9 - + - -
552B THR* 5.0 6.5 + - + +
569B ILE* 3.4 48.3 - - + +
571B SER* 4.4 8.7 - - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A MET* 3.5 32.5 - - + -
173A VAL 3.4 4.0 - - - +
174A GLN* 4.3 15.5 - - + +
186A SER* 4.4 1.6 - - - +
187A TYR* 1.3 75.0 - - - +
189A PHE* 1.3 72.0 + - - +
568B LEU* 3.8 37.0 - - + -
569B ILE 2.6 23.0 + - - +
570B VAL* 4.0 6.4 - - - -
571B SER 4.5 1.7 + - - -
572B ASP* 5.7 0.5 + - - +
577B PHE* 3.9 18.2 - - + -
579B PRO* 3.8 22.4 - - + +
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Residues in contact with PHE 189 (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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172A MET* 3.5 2.9 - - - -
173A VAL* 2.7 40.6 + - - +
175A VAL* 4.1 14.6 - - + -
187A TYR* 3.4 31.6 - - + -
188A VAL* 1.3 80.2 - - - +
190A ARG* 1.3 65.6 + - - +
191A GLY 3.3 0.2 + - - -
195A LEU* 3.6 22.9 - - + -
200A LEU* 4.1 12.3 - - + -
203A MET* 3.8 19.3 - - + -
204A LEU* 3.8 20.2 - - + -
270A ILE* 3.8 25.6 - - + -
571B SER* 3.4 26.2 - - - -
572B ASP* 5.8 4.9 - - + -
577B PHE* 4.2 5.6 - - - -
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Residues in contact with ARG 190 (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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172A MET* 4.1 13.8 - - - +
189A PHE* 1.3 75.0 - - - +
191A GLY* 1.3 58.4 + - - +
192A THR* 2.9 27.0 + - - +
193A LYS* 3.8 31.6 + - + +
195A LEU* 5.9 0.7 - - - +
266A VAL* 4.0 5.7 - - - +
572B ASP* 5.6 0.2 - - - -
575B ASP* 2.5 48.4 + - - -
576B VAL 3.5 6.3 + - - -
577B PHE* 3.0 57.5 - - + +
625B LYS* 5.8 2.0 - - - +
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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