Contacts of the strand formed by residues 2132 - 2138 (chain B) in PDB entry 1V9P
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 VAL2132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2011B ASN* 4.1 26.9 - - + +
2012B GLU* 4.2 18.2 - - + +
2015B ASP* 4.2 11.2 - - + +
2128B TYR* 2.9 5.4 - - - -
2129B GLU* 2.6 38.7 + - - +
2130B GLU* 3.9 11.9 - - + +
2131B GLY* 1.3 81.0 - - - +
2133B LEU* 1.3 74.9 + - - +
2134B VAL* 3.5 3.2 + - - +
2160B ARG 3.9 2.2 - - - -
2161B ARG* 3.6 35.9 - - - +
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Residues in contact with LEU2133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011B ASN* 4.6 4.3 - - - +
2015B ASP* 4.4 14.2 - - - +
2018B ARG* 4.7 4.1 + - - +
2126B LEU* 4.0 14.1 - - + -
2127B TYR 3.4 26.0 - - - +
2128B TYR* 3.3 26.6 - - + +
2132B VAL* 1.3 83.3 - - - +
2134B VAL* 1.3 64.5 + - - +
2135B PHE* 3.5 23.1 - - - +
2136B GLY* 5.7 0.7 - - - +
2149B THR* 5.6 8.1 - - + -
2152B LEU* 6.0 4.5 - - + -
2153B LEU* 4.6 20.6 - - + -
2158B ILE* 5.0 4.0 - - + -
2159B PRO 4.2 13.7 - - - +
2160B ARG* 3.2 17.0 + - + +
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Residues in contact with VAL2134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011B ASN* 3.9 22.9 - - + +
2014B ARG* 5.1 13.9 - - - +
2018B ARG* 2.6 34.1 + - - +
2058B ASP* 5.4 1.3 - - + +
2127B TYR* 2.7 38.9 + - + +
2129B GLU* 3.8 21.1 - - + +
2132B VAL 3.8 5.8 - - - +
2133B LEU* 1.3 77.3 - - - +
2135B PHE* 1.3 72.4 + - + +
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Residues in contact with PHE2135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2058B ASP* 4.6 10.3 - - + +
2074B ARG* 5.3 5.6 - - - -
2076B VAL* 3.8 30.7 - - + -
2077B ARG 4.9 1.3 - - - -
2078B HIS* 4.9 5.6 - - - -
2079B PRO* 4.3 18.8 - - + -
2125B ASN* 4.8 4.5 - - - -
2126B LEU* 3.8 0.2 - - - -
2127B TYR* 3.2 52.0 + + + -
2133B LEU* 3.5 8.4 - - - +
2134B VAL* 1.3 95.9 - - + +
2136B GLY* 1.3 63.3 + - - +
2137B ALA* 3.8 24.0 - - + -
2147B GLU* 4.4 14.1 - - + -
2149B THR* 3.1 13.2 - - - +
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Residues in contact with GLY2136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2125B ASN 3.4 9.0 - - - -
2126B LEU* 4.2 4.0 - - - -
2133B LEU* 5.2 1.1 - - - +
2135B PHE* 1.3 75.5 - - - +
2137B ALA* 1.3 61.4 + - - -
2147B GLU* 3.7 0.8 - - - -
2148B VAL* 2.8 28.4 + - - +
2149B THR* 2.7 16.8 + - - +
2152B LEU* 3.5 23.8 - - - -
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Residues in contact with ALA2137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2076B VAL* 4.5 6.7 - - + -
2078B HIS* 3.6 24.0 - - + +
2124B VAL* 3.5 3.3 - - - +
2125B ASN* 3.1 32.5 + - - +
2135B PHE* 3.8 19.9 - - + -
2136B GLY* 1.3 75.9 - - - +
2138B THR* 1.3 64.2 + - - +
2145B GLY 4.4 4.3 - - - -
2146B GLU 3.2 14.8 - - - +
2147B GLU* 4.0 3.6 - - - +
2148B VAL* 4.3 2.0 - - - -
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Residues in contact with THR2138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2078B HIS* 3.2 8.5 - - - -
2122B LEU* 5.3 3.8 - - + -
2123B SER 4.0 6.1 - - - -
2124B VAL* 4.4 3.1 - - - +
2137B ALA* 1.3 78.0 - - - +
2139B ARG* 1.3 64.5 + - - +
2140B GLY 3.9 4.7 + - - -
2145B GLY* 3.1 14.0 - - - -
2146B GLU* 2.4 63.7 + - + +
2148B VAL* 3.4 22.2 - - + -
2208B LEU* 3.9 18.2 - - + -
2209B ARG* 5.0 19.7 + - + +
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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