Contacts of the strand formed by residues 190 - 196 (chain Y) in PDB entry 3HI6
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 VAL 190 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148Y LYS 3.6 1.1 - - - +
149Y VAL* 3.4 8.8 - - - +
150Y ASP* 2.9 48.6 + - - +
151Y ASN* 5.5 6.7 - - - +
189Y LYS* 1.3 81.2 - - + +
191Y TYR* 1.3 70.1 + - - +
192Y ALA* 4.8 9.6 - - + -
207Y SER* 4.9 7.0 - - - -
208Y PHE 3.7 5.6 - - - +
209Y ASN* 3.3 20.6 - - - +
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Residues in contact with TYR 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y ILE* 3.5 5.7 - - - +
131Y VAL* 4.5 16.2 - - + -
147Y TRP* 5.2 2.7 - + + -
148Y LYS 3.8 1.6 - - - -
149Y VAL* 3.9 22.7 - - + +
178Y LEU* 4.7 6.1 - - + -
180Y LEU* 3.8 22.7 - - + +
184Y ASP 3.6 2.3 + - - -
185Y TYR* 2.6 53.2 + + - -
188Y HIS* 3.5 36.0 - - + +
189Y LYS 3.3 12.6 - - - -
190Y VAL* 1.3 72.4 - - - +
192Y ALA* 1.3 60.3 + - - +
207Y SER* 3.1 3.4 - - - -
208Y PHE* 2.9 66.6 + + + -
210Y ARG* 4.4 1.6 - - + -
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Residues in contact with ALA 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y ILE* 4.1 0.9 - - - -
146Y GLN 3.8 0.2 - - - +
147Y TRP* 3.5 11.7 - - - -
148Y LYS* 2.9 47.1 + - + +
190Y VAL* 4.8 7.4 - - + -
191Y TYR* 1.3 75.8 - - - +
193Y CYS* 1.3 60.6 + - - +
194Y GLU* 4.3 0.4 - - + -
205Y THR* 4.0 15.0 - - + -
206Y LYS 3.4 4.9 - - - -
207Y SER* 3.7 17.0 - - - -
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Residues in contact with CYS 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Y VAL* 4.4 5.8 - - - +
116Y ILE* 4.0 14.8 - - - +
133Y CYS* 2.0 55.4 - - + -
145Y VAL* 4.3 4.7 - - + -
146Y GLN 3.2 7.4 - - - +
147Y TRP* 4.0 14.4 - - + -
192Y ALA* 1.3 74.7 - - - +
194Y GLU* 1.3 60.5 + - - +
195Y VAL* 4.1 1.0 + - - +
204Y VAL 3.7 1.7 - - - +
205Y THR* 3.4 3.9 - - - -
206Y LYS* 3.0 39.6 + - - -
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Residues in contact with GLU 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y LYS* 3.5 2.4 - - - +
145Y VAL* 3.5 3.9 - - - -
146Y GLN* 2.8 63.1 + - + +
148Y LYS* 5.5 14.2 - - + +
192Y ALA* 4.3 0.4 - - + -
193Y CYS* 1.3 73.1 - - - +
195Y VAL* 1.3 62.7 + - - +
196Y THR* 3.9 6.9 + - - -
203Y PRO* 3.7 29.9 - - + +
204Y VAL 3.3 3.1 - - - +
205Y THR* 3.3 22.2 + - + +
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Residues in contact with VAL 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Y PRO* 4.0 18.6 - - + -
114Y VAL* 3.5 33.7 - - + -
133Y CYS* 4.4 6.3 - - - -
135Y LEU* 3.6 43.1 - - + -
144Y LYS 3.5 3.8 - - - +
145Y VAL* 4.4 5.6 - - + -
194Y GLU* 1.3 77.2 - - - +
196Y THR* 1.3 67.9 + - - +
197Y HIS* 4.6 0.4 - - + -
200Y LEU* 4.0 9.1 - - + +
203Y PRO* 3.1 7.4 - - - +
204Y VAL* 2.7 36.8 + - + +
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Residues in contact with THR 196 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y ALA* 3.6 3.6 - - - +
144Y LYS* 2.9 58.1 + - + +
194Y GLU* 3.9 8.9 + - - -
195Y VAL* 1.3 75.0 + - - +
197Y HIS* 1.3 68.5 + - - +
200Y LEU* 5.8 0.2 - - - -
202Y SER 6.1 0.4 - - - -
203Y PRO* 4.0 22.5 - - + +
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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