Contacts of the strand formed by residues 195 - 199 (chain D) in PDB entry 3NY5
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 CYS 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D LEU* 4.4 4.3 - - - -
190D LEU* 4.1 23.6 - - - -
191D ILE 3.8 11.0 - - - +
192D PRO 3.1 17.9 + - - +
193D GLU 3.4 0.5 - - - -
194D CYS* 1.3 95.0 - - - +
196D ALA* 1.3 60.2 + - - +
210D TRP* 3.1 14.4 + - + -
224D VAL* 3.8 23.6 - - + -
225D GLU 3.0 17.9 - - - +
226D VAL* 4.3 4.9 - - - -
227D LEU* 3.8 12.9 - - - +
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Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D CYS* 1.3 75.3 - - - +
197D VAL* 1.3 61.9 + - - +
198D TYR* 3.4 31.0 - - + +
207D PRO* 6.4 0.7 - - + -
210D TRP* 4.1 4.7 - - - +
223D HIS 3.7 0.5 - - - +
224D VAL* 3.3 6.1 - - - +
225D GLU* 2.8 35.7 + - + +
227D LEU* 3.9 16.2 - - + +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D VAL* 4.2 18.4 - - + -
196D ALA* 1.3 76.4 - - - +
198D TYR* 1.3 75.4 + - - +
207D PRO* 3.6 3.6 - - - +
208D ILE* 3.0 56.1 + - + +
210D TRP* 3.7 41.4 - - + +
222D LEU* 4.2 14.1 - - + -
223D HIS 3.3 9.4 - - - +
224D VAL* 4.3 8.1 - - + -
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Residues in contact with TYR 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ALA* 3.4 35.7 - - + +
197D VAL* 1.3 72.6 - - - +
199D ARG* 1.3 67.1 + - - +
205D LYS* 3.8 41.7 - - + -
206D LYS 3.3 9.0 - - - +
207D PRO* 3.6 33.4 - - + -
208D ILE* 4.3 2.0 - - - +
222D LEU* 3.0 12.9 - - - +
223D HIS* 2.8 43.1 + - + +
225D GLU* 3.6 30.9 + - + -
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D TYR* 1.3 76.3 - - - +
200D ILE* 1.3 74.8 + - - +
205D LYS* 3.6 0.2 - - - -
206D LYS* 2.9 56.9 + - + +
208D ILE* 3.9 20.4 - - + +
216D TRP 5.5 2.2 + - - -
217D LEU* 4.2 18.4 - - + +
220D GLU* 3.1 38.7 + - + +
221D GLU 3.6 7.4 - - - +
222D LEU* 3.8 13.7 - - + -
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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