Contacts of the strand formed by residues 195 - 199 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 4.6 2.2 - - - -
190B LEU* 4.2 15.5 - - - -
191B ILE 3.3 16.8 - - - +
192B PRO 2.9 17.3 + - - +
193B GLU 3.3 0.9 - - - -
194B CYS* 1.3 94.2 - - - +
196B ALA* 1.3 60.7 + - - +
210B TRP* 2.9 15.1 + - + -
224B VAL* 3.7 23.8 - - + -
225B GLU 3.1 14.6 - - - +
226B VAL* 4.2 12.6 - - - -
227B LEU* 3.8 13.6 - - - +
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PRO* 3.9 32.1 - - + -
195B CYS* 1.3 72.8 - - - +
197B VAL* 1.3 61.4 + - - +
198B TYR* 4.0 17.1 - - + +
207B PRO* 6.4 0.2 - - + -
210B TRP* 4.1 4.9 - - - +
223B HIS 3.8 0.5 - - - +
224B VAL* 3.3 6.1 - - - +
225B GLU 2.7 34.2 + - - +
227B LEU* 4.0 6.2 - - + +
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Residues in contact with VAL 197 (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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177B VAL* 4.2 16.4 - - + -
181B LEU* 4.8 0.4 - - + -
196B ALA* 1.3 76.7 - - - +
198B TYR* 1.3 74.7 + - - +
207B PRO* 3.5 5.2 - - - +
208B ILE* 2.8 62.6 + - + +
210B TRP* 3.6 42.1 - - + +
222B LEU* 4.2 15.0 - - + -
223B HIS 3.4 9.2 - - - +
224B VAL* 4.4 8.5 - - + -
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Residues in contact with TYR 198 (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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198A TYR* 3.0 45.3 - + - -
205A LYS 4.9 0.7 + - - -
207A PRO* 3.3 21.5 - - - +
196B ALA* 4.0 18.3 - - + +
197B VAL* 1.3 75.1 - - - +
199B ARG* 1.3 65.1 + - - +
200B ILE* 5.9 0.2 - - + -
205B LYS* 4.2 17.9 - - + -
206B LYS 3.2 14.8 - - - +
207B PRO* 3.5 23.1 - - + -
208B ILE* 4.2 2.7 - - - +
222B LEU* 3.1 11.4 - - - +
223B HIS* 2.8 50.7 + - + +
225B GLU* 3.7 29.3 + - + -
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Residues in contact with ARG 199 (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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228A GLU* 3.3 36.2 + - - +
229A ASN 5.5 1.4 + - - +
230A VAL* 4.2 15.5 - - - +
198B TYR* 1.3 75.3 - - - +
200B ILE* 1.3 68.9 + - - +
201B GLN* 3.4 22.1 + - + +
204B GLU 3.4 2.4 - - - +
205B LYS* 3.7 2.1 - - - -
206B LYS* 2.8 37.1 + - + +
208B ILE* 3.8 10.1 - - + +
216B TRP 5.3 3.0 + - - -
217B LEU* 4.4 18.3 - - + +
220B GLU* 3.4 34.5 + - - +
221B GLU 3.7 0.4 - - - -
222B LEU* 3.6 20.0 - - + -
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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