Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 1VI7
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LEU 3.8 1.0 - - - +
145A GLN* 3.3 9.5 - - - +
146A CYS* 2.7 46.3 + - - +
147A GLU 4.2 1.3 - - - -
148A TYR* 3.8 44.9 - - + +
151A LEU* 4.0 9.4 - - + -
169A ASP 3.6 2.7 - - - +
170A TYR* 3.7 24.0 - - + -
171A GLN* 3.8 0.4 - - - -
173A PHE* 1.3 76.2 - - - +
175A LEU* 1.3 63.4 + - - +
176A LEU* 3.7 28.5 - - + -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 4.9 14.1 - - + +
144A LEU 4.3 6.7 - - - +
145A GLN* 3.8 32.5 - - + +
167A ASN* 3.8 2.4 - - - +
168A SER* 3.6 2.9 - - - -
169A ASP* 2.9 46.2 + - + +
171A GLN* 3.1 22.8 - - - +
174A VAL* 1.3 72.8 - - - +
176A LEU* 1.3 68.9 + - - +
177A ARG* 6.4 0.7 - - + -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 3.2 8.9 - - - +
144A LEU* 2.9 49.0 + - + +
146A CYS* 4.3 20.9 - - - -
151A LEU* 4.1 11.2 - - + -
154A ILE* 4.3 22.4 - - + -
155A GLU* 6.3 0.2 - - + -
165A ILE* 3.6 28.0 - - + -
167A ASN 3.7 1.6 - - - -
168A SER* 3.6 24.7 - - - +
174A VAL* 3.7 21.5 - - + -
175A LEU* 1.3 76.5 - - - +
177A ARG* 1.3 59.2 + - - +
178A VAL* 3.9 9.9 - - + -
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 3.2 28.4 + - - +
142A TYR 3.4 15.3 - - - -
143A THR* 3.9 12.3 - - + +
165A ILE* 3.9 1.9 - - - +
166A ILE* 2.9 36.0 + - + +
167A ASN* 3.2 46.4 + - - +
175A LEU* 6.4 0.7 - - + -
176A LEU* 1.3 72.5 - - - +
178A VAL* 1.3 59.2 + - - +
205A ILE* 3.2 32.3 - - - +
208A GLU* 5.0 7.3 + - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 3.2 4.2 - - - +
142A TYR* 2.6 64.7 + - + +
144A LEU* 4.6 12.3 - - + -
154A ILE* 5.5 1.1 - - + -
158A LEU* 3.6 39.5 - - + -
164A LYS 3.7 3.1 - - - -
165A ILE* 4.2 4.3 - - - -
166A ILE* 4.4 1.8 - - - -
176A LEU* 3.9 22.2 - - + -
177A ARG* 1.3 77.3 - - - +
179A ALA* 1.3 59.4 + - - +
180A LEU* 4.5 7.9 - - + -
188A PHE* 5.1 0.9 - - + -
202A LEU* 4.0 16.8 - - + -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.0 23.2 - - + +
140A THR 3.0 12.3 - - - +
141A GLU* 4.1 9.2 - - + +
163A GLY* 3.3 0.9 - - - -
164A LYS* 2.8 44.7 + - + +
166A ILE* 3.9 21.1 - - + -
178A VAL* 1.3 76.4 - - - +
180A LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.0 4.0 - - - -
140A THR* 2.9 28.5 + - - +
142A TYR* 3.5 30.4 - - + -
158A LEU* 4.8 2.9 - - + -
161A CYS* 4.4 4.3 - - + +
163A GLY* 3.7 13.0 - - - -
178A VAL* 4.5 11.2 - - + -
179A ALA* 1.3 82.5 - - - +
181A PRO* 1.3 86.1 - - + +
182A ALA* 3.3 0.3 + - - -
184A LYS* 4.1 4.9 - - + -
185A VAL* 3.8 21.5 - - + +
188A PHE* 3.8 43.5 - - + -
202A LEU* 5.3 0.9 - - + -
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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