Contacts of the strand formed by residues 194 - 200 (chain Y) in PDB entry 4MXV
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 TYR 194 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138Y LEU* 3.7 37.2 - - + -
154Y TRP* 4.2 5.4 - + + -
155Y ASN* 3.6 8.3 - - - -
159Y LEU* 3.6 33.0 - - + -
182Y VAL* 5.3 0.2 - - + -
184Y VAL* 3.4 33.8 - - + +
185Y PRO* 5.3 0.3 - - - +
188Y SER* 3.2 31.9 + - - -
189Y LEU* 4.4 8.3 - - + -
192Y GLN* 3.6 33.7 - - + +
193Y THR* 1.3 72.7 - - - +
195Y ILE* 1.3 63.1 + - - +
210Y LYS* 3.7 2.8 - - - +
211Y VAL* 3.0 37.8 + - - +
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Residues in contact with ILE 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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154Y TRP* 3.3 8.5 - - - -
155Y ASN* 2.8 48.9 + - - +
193Y THR* 4.6 9.9 - - - +
194Y TYR* 1.3 79.4 - - - +
196Y CYS* 1.3 70.0 + - - +
197Y ASN* 4.0 13.3 + - - +
208Y ASP* 4.2 8.7 - - + -
209Y LYS 3.4 23.1 - - - +
210Y LYS* 4.1 22.2 - - + +
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Residues in contact with CYS 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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121Y VAL* 4.3 3.8 - - - -
140Y CYS* 1.5 58.1 - - + -
152Y VAL* 4.4 7.0 - - + -
153Y SER 3.5 6.1 - - - +
154Y TRP* 3.5 27.0 - - + -
195Y ILE* 1.3 73.8 - - - +
197Y ASN* 1.3 61.2 + - - +
198Y VAL* 4.0 3.0 - - + +
207Y VAL 3.7 1.9 - - - +
208Y ASP* 3.5 2.9 - - - -
209Y LYS* 3.1 45.5 + - - -
211Y VAL* 4.6 0.2 - - - -
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Residues in contact with ASN 197 (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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151Y THR* 3.3 2.4 - - - +
152Y VAL* 3.3 5.2 - - - -
153Y SER* 2.6 56.6 + - - +
155Y ASN 3.8 0.9 + - - -
156Y SER* 3.0 36.2 + - - +
195Y ILE* 4.1 12.7 + - - +
196Y CYS* 1.3 75.8 - - - +
198Y VAL* 1.3 62.2 + - - +
199Y ASN* 3.9 0.8 + - - -
206Y LYS* 5.4 9.2 - - - -
208Y ASP* 3.0 31.7 + - - +
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Residues in contact with VAL 198 (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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119Y PRO* 4.3 7.3 - - + +
121Y VAL* 3.7 28.0 - - + -
140Y CYS* 5.1 0.2 - - + -
142Y VAL* 3.7 40.6 - - + -
150Y VAL* 3.9 20.6 - - + -
151Y THR 3.2 7.4 - - - +
152Y VAL* 4.1 11.0 - - + -
196Y CYS* 4.7 7.9 - - - +
197Y ASN* 1.3 76.5 - - - +
199Y ASN* 1.3 59.9 + - - +
205Y THR* 4.1 0.9 - - - +
206Y LYS* 3.4 5.2 - - - +
207Y VAL* 2.9 42.5 + - + +
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Residues in contact with ASN 199 (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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149Y PRO 4.3 0.3 - - - +
150Y VAL* 3.4 5.5 - - - +
151Y THR* 2.8 56.5 + - + +
197Y ASN 3.9 1.4 + - - -
198Y VAL* 1.3 73.9 - - - +
200Y HIS* 1.3 66.8 + - - +
201Y LYS* 3.8 37.3 + - - +
205Y THR 3.6 7.3 - - - +
206Y LYS* 3.7 26.9 - - + +
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Residues in contact with HIS 200 (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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117Y LYS 3.2 24.0 - - - -
118Y GLY* 3.6 6.7 - - - -
119Y PRO* 3.7 21.1 - - + +
145Y TYR* 4.0 3.2 - + + -
146Y PHE 3.4 11.7 - - - -
147Y PRO 2.9 22.3 + - - -
149Y PRO 3.2 25.4 - - - -
150Y VAL* 3.7 13.2 - - + -
199Y ASN* 1.3 76.6 + - - +
201Y LYS* 1.3 60.7 + - - +
202Y PRO* 3.4 14.5 - - + +
203Y SER* 2.6 50.7 + - - +
205Y THR 2.7 22.4 + - - +
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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