Contacts of the strand formed by residues 2171 - 2178 (chain A) in PDB entry 5W0P
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 VAL2171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2016A LYS* 3.6 45.5 - - + +
2017A VAL 4.0 7.0 - - - +
2018A SER* 3.9 10.5 - - - +
2023A VAL* 3.9 21.5 - - + +
2025A ILE* 4.2 14.9 - - + +
2150A VAL 4.3 0.2 - - - +
2151A LYS* 3.4 2.8 - - - +
2152A ALA* 2.7 59.0 + - + +
2170A SER* 1.3 77.8 - - - +
2172A ARG* 1.3 65.3 + - - +
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Residues in contact with ARG2172 (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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336A TPO 3.5 32.1 + - - +
338A SEP 4.3 0.2 + - - -
2016A LYS* 3.0 32.8 + - - +
2025A ILE* 5.7 1.1 - - - -
2067A ARG* 6.3 0.2 - - - -
2149A GLU* 3.3 31.0 + - - +
2150A VAL 3.5 5.4 - - - -
2151A LYS* 3.7 31.8 - - + +
2171A VAL* 1.3 79.9 - - - +
2173A LEU* 1.3 61.0 + - - +
2174A LEU* 6.5 0.2 - - + -
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Residues in contact with LEU2173 (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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338A SEP 4.4 13.9 - - - +
2014A PHE* 4.2 26.2 - - + -
2015A LYS* 5.1 6.1 - - - +
2016A LYS* 4.6 15.3 - - + +
2025A ILE* 5.2 10.8 - - + -
2027A LEU* 3.9 20.9 - - + -
2030A ARG* 3.8 25.8 - - + +
2149A GLU* 4.5 3.4 - - - -
2150A VAL* 2.9 35.4 + - - +
2172A ARG* 1.3 77.2 - - - +
2174A LEU* 1.3 84.6 + - - +
2175A ILE* 3.7 16.3 + - + +
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Residues in contact with LEU2174 (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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338A SEP 5.2 3.4 + - - +
2030A ARG* 3.6 18.9 + - - +
2067A ARG* 4.9 6.1 - - - +
2147A ASP* 3.7 25.6 - - + +
2148A PHE 3.7 12.1 - - - +
2149A GLU* 3.6 26.7 - - + +
2172A ARG* 6.5 0.2 - - + -
2173A LEU* 1.3 87.1 - - - +
2175A ILE* 1.3 61.6 + - - +
2299A LYS 5.9 1.6 - - - +
2300A ILE* 4.6 12.5 - - + +
2301A LYS* 5.3 12.6 - - - +
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Residues in contact with ILE2175 (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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2027A LEU* 4.2 4.7 - - + -
2029A LYS 4.6 0.2 - - - +
2030A ARG* 3.3 19.1 - - - +
2032A TYR* 3.8 27.8 - - + -
2042A VAL* 3.8 11.9 - - + -
2062A LEU* 4.1 9.2 - - + -
2123A PHE* 4.2 5.6 - - + -
2130A SER* 4.2 1.2 + - - -
2147A ASP* 5.3 0.9 - - - +
2148A PHE* 3.1 43.6 + - + +
2150A VAL* 3.5 36.3 - - + -
2173A LEU* 3.8 17.0 - - + +
2174A LEU* 1.3 79.7 - - - +
2176A ARG* 1.3 67.7 + - - +
2300A ILE* 4.8 1.3 - - - -
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Residues in contact with ARG2176 (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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2030A ARG 2.8 10.0 + - - +
2031A ASP* 2.9 43.6 + - - +
2032A TYR* 2.8 35.9 + - - +
2130A SER* 3.4 13.5 - - - +
2148A PHE* 4.9 1.8 - - - -
2175A ILE* 1.3 79.4 - - - +
2177A LYS* 1.3 56.6 - - - +
2178A VAL* 3.9 21.5 - - + +
2297A ASP* 4.8 8.5 - - - +
2298A GLY* 2.8 45.0 + - - +
2299A LYS* 4.9 0.4 - - - +
2300A ILE* 3.5 27.8 - - + +
2303A GLU* 3.9 17.6 + - - -
2305A THR* 4.9 4.2 + - - -
2306A ASN* 5.9 0.2 + - - -
2358A HIS* 5.9 3.6 - - - -
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Residues in contact with LYS2177 (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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2032A TYR* 3.5 7.4 - - + +
2034A ASP* 2.9 46.7 + - + +
2039A VAL* 3.7 22.9 - - + +
2123A PHE* 4.2 17.5 - - + -
2124A PRO 5.0 1.3 + - - -
2125A ASP 6.4 0.2 - - - -
2127A LEU* 3.3 25.3 + - - +
2128A PRO 3.3 16.6 + - - +
2129A CYS* 3.3 10.3 - - - +
2130A SER* 2.9 29.7 + - - -
2148A PHE* 3.6 39.8 - - + -
2176A ARG* 1.3 71.9 - - - +
2178A VAL* 1.3 60.3 + - - +
2179A GLN* 4.9 0.2 - - - +
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Residues in contact with VAL2178 (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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2031A ASP* 4.9 10.5 - - + -
2032A TYR 3.1 9.9 + - - +
2033A VAL* 3.5 6.9 - - - +
2034A ASP 2.7 29.6 + - - -
2129A CYS* 4.8 2.0 - - - -
2130A SER* 5.4 3.8 - - - +
2176A ARG* 3.9 37.9 - - + +
2177A LYS* 1.3 78.3 - - - +
2179A GLN* 1.3 71.2 + - - +
2180A HIS* 3.9 15.8 + - + +
2297A ASP* 5.8 6.1 - - + +
2309A SER* 5.3 3.6 - - - +
2358A HIS* 4.5 20.0 - - + +
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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