Contacts of the strand formed by residues 194 - 200 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138F LEU* 3.6 35.9 - - + -
154F TRP* 4.5 4.0 - - + -
155F ASN* 3.4 12.3 - - - -
159F LEU* 3.5 29.8 - - + -
184F VAL* 3.4 38.1 - - + +
185F PRO* 5.3 0.3 - - - +
188F SER* 3.0 28.9 + - - -
189F LEU* 4.1 12.1 - - + -
192F GLN* 3.3 38.3 - - + +
193F THR* 1.3 72.4 - - - +
195F ILE* 1.3 62.6 + - - +
210F LYS* 3.7 4.4 - - - +
211F VAL* 3.0 35.1 + - - +
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Residues in contact with ILE 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F TRP* 3.1 10.2 - - - -
155F ASN* 2.8 38.7 + - - +
193F THR* 5.2 7.6 - - - +
194F TYR* 1.3 80.2 - - - +
196F CYS* 1.3 75.0 + - - +
197F ASN* 4.1 8.1 - - - +
208F ASP* 3.7 15.9 - - + -
209F LYS 3.6 19.3 - - - +
210F LYS* 4.0 26.9 - - + +
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Residues in contact with CYS 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F VAL* 4.1 0.7 - - - -
140F CYS* 2.0 48.5 - - + -
152F VAL* 4.4 5.4 - - + -
153F SER 3.3 7.6 - - - +
154F TRP* 3.6 20.7 - - + -
195F ILE* 1.3 75.6 - - - +
197F ASN* 1.3 60.8 + - - +
198F VAL* 4.0 15.3 - - - -
207F VAL 3.7 1.2 - - - +
208F ASP* 3.2 5.0 - - - -
209F LYS* 3.0 43.7 + - - -
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Residues in contact with ASN 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F THR* 3.5 3.5 - - - +
152F VAL* 3.5 2.9 - - - -
153F SER* 2.7 58.1 + - - +
155F ASN 3.4 2.6 + - - -
156F SER* 2.9 39.7 + - - +
195F ILE* 4.1 10.7 + - - +
196F CYS* 1.3 74.4 - - - +
198F VAL* 1.3 62.9 + - - +
199F ASN* 3.9 0.9 + - - +
206F LYS* 6.2 4.7 - - + -
208F ASP* 3.0 31.8 + - - +
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Residues in contact with VAL 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F PRO* 4.6 9.9 - - + -
121F VAL* 3.7 22.7 - - + -
142F VAL* 3.7 41.5 - - + -
150F VAL* 4.2 7.9 - - + -
151F THR 3.3 7.0 - - - +
152F VAL* 4.2 9.4 - - + -
196F CYS* 4.0 20.9 - - - -
197F ASN* 1.3 74.1 - - - +
199F ASN* 1.3 66.2 + - - +
205F THR* 4.2 1.0 - - + +
206F LYS* 3.4 6.3 - - - +
207F VAL* 2.8 43.6 + - + +
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Residues in contact with ASN 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F PRO 4.3 0.3 - - - +
150F VAL* 3.3 7.3 - - - +
151F THR* 2.7 55.4 + - + +
197F ASN 5.2 0.9 - - - +
198F VAL* 1.3 75.4 - - - +
200F HIS* 1.3 68.3 + - - +
201F LYS* 3.5 42.4 + - - +
204F ASN* 5.4 0.9 - - - -
205F THR 3.2 10.2 - - - +
206F LYS* 4.0 28.9 - - + +
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Residues in contact with HIS 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LYS 3.3 22.7 - - - -
119F PRO* 3.7 27.6 - - + +
145F TYR* 3.8 6.5 - + + -
146F PHE 3.4 12.1 + - - -
147F PRO 2.8 24.4 + - - -
149F PRO 3.4 20.4 - - - -
150F VAL* 3.7 15.7 - - + -
198F VAL* 4.3 0.6 - - - +
199F ASN* 1.3 72.7 + - - +
201F LYS* 1.3 64.6 + - - +
202F PRO* 3.2 14.6 - - + +
203F SER* 2.8 38.3 + - - -
204F ASN 3.3 6.4 + - - -
205F THR* 2.9 17.8 + - - +
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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