Contacts of the strand formed by residues 150 - 155 (chain L) in PDB entry 3VI4
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 ASN 150 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L ILE* 1.3 82.3 - - - +
151L VAL* 1.3 72.2 + - - +
152L LYS* 5.4 8.3 - - - +
180L MET* 5.9 0.7 - - - -
200L GLU 3.2 3.5 - - - +
201L ALA* 3.3 3.5 - - - -
202L THR* 2.9 52.3 + - - +
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Residues in contact with VAL 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L CYS* 5.1 1.8 - - - -
141L LEU* 3.5 17.3 - - + -
150L ASN* 1.3 84.5 + - - +
152L LYS* 1.3 74.7 + - - +
153L TRP* 4.3 7.0 + - + +
166L ASN* 5.1 3.9 + - - +
180L MET* 3.5 39.1 - - + +
182L SER* 4.0 24.7 - - - +
199L CYS* 4.1 18.4 - - + -
200L GLU 3.4 6.5 - - - +
201L ALA* 5.0 0.9 - - - -
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Residues in contact with LYS 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L ASN* 5.4 8.6 - - - +
151L VAL* 1.3 77.6 - - - +
153L TRP* 1.3 62.9 + - - +
154L LYS* 4.1 22.2 - - + +
159L GLU* 3.3 42.5 + - + +
198L THR 3.6 0.9 - - - +
199L CYS* 3.4 4.9 - - - -
200L GLU* 2.8 57.1 + - + +
202L THR* 6.2 4.5 - - + -
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Residues in contact with TRP 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L ILE* 3.9 14.8 - - + -
137L VAL* 3.4 45.3 - - + -
139L CYS* 3.6 28.7 - - + -
151L VAL* 4.3 7.2 + - + +
152L LYS* 1.3 76.5 - - - +
154L LYS* 1.3 63.3 + - - +
155L ILE* 4.3 0.4 - - + -
159L GLU* 3.3 9.2 - - - +
160L ARG* 3.0 43.7 + - + +
161L GLN* 6.2 1.2 - - - +
164L VAL* 3.7 30.6 - - + +
182L SER* 3.2 32.8 + - - -
183L THR 4.5 0.2 - - - +
184L LEU* 4.0 29.1 - - + +
197L TYR* 4.5 2.9 - - + -
198L THR 3.4 25.6 - - - -
199L CYS* 4.1 5.6 - - + -
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Residues in contact with LYS 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L LYS* 4.1 19.6 - - + +
153L TRP* 1.3 81.3 - - - +
155L ILE* 1.3 63.1 + - - +
156L ASP 4.1 0.4 + - - -
157L GLY* 3.7 27.2 + - - +
158L SER 3.3 11.7 - - - +
159L GLU* 4.1 9.1 - - + +
196L SER 3.7 0.7 - - - +
197L TYR* 3.4 4.5 - - - -
198L THR* 2.8 55.4 + - + +
200L GLU* 3.3 35.9 + - - +
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Residues in contact with ILE 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L TRP* 5.5 0.4 - - + -
154L LYS* 1.3 75.3 - - - +
156L ASP* 1.3 71.4 + - - +
157L GLY 3.2 0.7 + - - -
158L SER* 3.0 22.9 + - - +
160L ARG* 4.0 33.9 + - + +
184L LEU* 3.8 26.0 - - + -
186L LEU* 4.5 13.7 - - + -
194L HIS* 3.4 44.9 - - + +
196L SER 3.4 4.0 - - - +
197L TYR* 3.7 26.0 - - + -
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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