Contacts of the helix formed by residues 2124 - 2128 (chain A) in PDB entry 4UXL
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 PRO2124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2078A ARG 5.7 2.7 - - - +
2079A ASP* 3.7 22.4 - - - +
2083A ARG* 3.8 16.4 - - - +
2105A LEU* 5.9 2.0 - - + -
2122A LEU* 3.9 10.3 - - + -
2123A LEU* 1.3 90.2 - - + +
2125A VAL* 1.3 64.5 + - - +
2126A ARG 3.2 3.1 - - - -
2127A TRP* 3.2 32.5 + - + -
2128A MET* 3.1 30.3 + - + +
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Residues in contact with VAL2125 (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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2123A LEU* 2.6 21.9 + - - +
2124A PRO* 1.3 73.2 - - - +
2126A ARG* 1.3 63.1 + - + +
2127A TRP 3.3 1.0 + - - -
2128A MET* 3.3 21.0 + - - +
2133A LEU* 3.8 33.8 - - + +
2167A ASN* 4.1 29.6 - - + +
2170A VAL* 3.9 22.4 - - + +
2171A LEU* 4.5 12.1 - - + +
2174A VAL* 5.9 0.7 - - - +
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Residues in contact with ARG2126 (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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2124A PRO 3.2 0.8 - - - -
2125A VAL* 1.3 79.3 - - + +
2127A TRP* 1.3 79.3 + - + +
2128A MET 3.6 0.7 - - - -
2145A TRP* 4.9 1.0 + - - -
2149A ILE* 3.8 16.1 - - - +
2160A GLN* 3.7 34.5 + - - +
2161A PRO* 2.8 30.0 + - + -
2162A TYR* 2.6 69.7 + - + +
2165A HIS 2.7 20.6 + - - -
2166A SER* 3.6 1.8 - - - +
2167A ASN* 3.1 37.7 + - - +
2170A VAL* 3.8 11.5 - - + +
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Residues in contact with TRP2127 (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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2035A LEU* 6.3 1.1 - - + -
2079A ASP* 5.5 3.4 - - - +
2080A LEU 3.4 24.0 - - - +
2081A ALA* 3.4 4.7 - - + +
2083A ARG* 3.0 34.3 - - - -
2124A PRO* 3.2 23.0 + - + +
2125A VAL 3.2 0.6 - - - -
2126A ARG* 1.3 100.8 - - + +
2128A MET* 1.3 59.6 + - + +
2145A TRP* 3.4 10.9 - - - -
2146A SER* 2.4 34.2 + - - +
2149A ILE* 3.4 33.4 - - + +
2153A GLU* 3.0 41.0 + - - -
2160A GLN* 4.7 8.1 - - - -
2161A PRO* 4.0 19.7 - - + -
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Residues in contact with MET2128 (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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2078A ARG 5.9 2.5 - - - +
2122A LEU* 3.8 35.0 - - + -
2123A LEU 5.0 1.6 - - - -
2124A PRO* 3.1 38.6 - - + +
2125A VAL* 3.3 8.0 + - - +
2126A ARG 5.3 0.3 - - - -
2127A TRP* 1.3 78.3 - - + +
2129A ALA* 1.3 65.6 + - - +
2130A PRO 3.7 0.2 - - - -
2132A SER* 4.0 15.9 - - - +
2133A LEU* 3.4 57.8 - - + +
2138A PHE* 4.1 8.3 - - + -
2145A TRP* 3.3 13.3 + - - -
2146A SER* 4.5 1.6 - - - +
2174A VAL* 5.2 4.0 - - - +
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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