Contacts of the helix formed by residues 2127 - 2132 (chain B) in PDB entry 2ASS
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 TRP2127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127A ILE* 4.3 15.5 - - + -
1135A ILE* 4.2 16.4 - - + -
1139A PHE* 5.0 7.0 - + - -
1141A ILE* 4.9 21.9 - - + +
2097B TRP* 6.4 1.1 - - + -
2098B ASP* 5.4 6.7 + - - +
2105B LEU* 3.4 44.3 - - + +
2108B ILE* 6.4 0.4 - - + -
2109B PHE* 3.6 28.5 - + - -
2120B VAL* 3.6 41.7 - - + +
2123B VAL* 3.6 22.4 - - + -
2124B CYS* 3.1 39.7 - - - +
2126B ARG* 1.5 82.0 - - - +
2128B TYR* 1.3 56.0 + - - -
2129B ARG 3.4 0.4 - - - -
2130B LEU* 4.0 4.3 - - - +
2131B ALA* 3.1 26.2 + - - +
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Residues in contact with TYR2128 (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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1145A PHE* 4.0 11.0 - + + -
1153A VAL* 3.7 34.1 - - + -
1156A GLU* 3.4 23.4 + - - -
1157A ASN* 5.8 0.9 - - - -
2121B SER* 2.8 41.2 + - - +
2124B CYS 3.0 11.5 + - - +
2125B LYS* 4.2 19.7 - - + -
2127B TRP* 1.3 78.2 - - - +
2129B ARG* 1.3 72.8 + - + +
2131B ALA* 3.4 10.2 + - - +
2132B SER* 3.6 23.2 + - - -
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Residues in contact with ARG2129 (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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2102B ASP* 4.2 17.8 + - - -
2125B LYS* 5.8 1.6 - - + -
2126B ARG* 1.6 48.5 + - - +
2128B TYR* 1.3 93.2 - - + +
2130B LEU* 1.3 63.4 + - + +
2132B SER* 3.7 10.5 + - - +
2133B ASP* 4.0 7.4 + - - +
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Residues in contact with LEU2130 (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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2102B ASP* 3.7 34.8 - - + +
2105B LEU* 3.4 41.5 - - + -
2106B LEU* 3.7 24.2 - - + +
2109B PHE* 3.7 15.5 - - + -
2126B ARG* 3.0 23.2 + - + +
2127B TRP* 3.9 3.6 + - - +
2128B TYR 3.3 0.4 - - - -
2129B ARG* 1.3 79.7 - - + +
2131B ALA* 1.3 56.2 + - - +
2132B SER 2.9 5.6 - - - -
2133B ASP* 2.7 37.2 + - - +
2136B LEU* 3.4 6.9 - - - +
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Residues in contact with ALA2131 (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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2109B PHE* 3.8 7.1 - - + -
2117B LEU* 3.6 35.6 - - + +
2118B LEU* 6.2 0.2 - - - +
2120B VAL* 4.5 0.9 - - + -
2121B SER* 3.8 27.1 - - - +
2127B TRP 3.1 19.1 + - - +
2128B TYR 3.4 7.5 + - - +
2130B LEU* 1.3 76.9 - - - +
2132B SER* 1.3 58.5 + - - +
2133B ASP 3.4 0.9 - - - -
2136B LEU* 4.2 2.3 - - - +
2137B TRP* 3.3 17.7 + - - -
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Residues in contact with SER2132 (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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2121B SER* 5.1 3.6 + - - -
2128B TYR* 3.6 21.7 + - - -
2129B ARG* 3.7 7.4 + - - +
2130B LEU 2.9 0.8 - - - -
2131B ALA* 1.3 79.3 + - - +
2133B ASP* 1.3 70.0 + - - +
2137B TRP* 3.8 12.9 + - - +
2158B GLN* 3.4 30.7 + - - +
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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