Contacts of the strand formed by residues 2184 - 2188 (chain B) in PDB entry 1F38
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 VAL2184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2148B THR* 4.0 18.2 - - + -
2152B ALA* 3.8 21.1 - - + -
2157B ARG* 4.2 4.0 + - - -
2158B VAL* 3.3 15.5 - - + +
2160B ALA* 4.4 3.6 - - + -
2175B LEU* 4.1 9.6 - - + -
2181B GLY* 3.5 29.3 - - - +
2182B ASP 3.1 4.7 - - - +
2183B ASN* 1.3 94.3 - - - +
2185B THR* 1.3 62.9 + - - +
2186B LEU* 3.9 29.1 + - + +
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Residues in contact with THR2185 (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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2157B ARG* 2.7 32.5 + - - +
2158B VAL 2.9 8.7 + - - -
2159B TYR* 3.7 29.2 - - + -
2160B ALA 3.0 24.1 + - - +
2184B VAL* 1.3 71.2 - - - +
2186B LEU* 1.3 64.7 + - - +
2187B MSE 3.7 21.6 + - + +
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Residues in contact with LEU2186 (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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2142B CYS* 5.5 0.2 - - - -
2160B ALA* 3.7 16.2 - - + +
2168B ILE* 3.9 31.0 - - + +
2171B THR* 4.3 15.9 - - + -
2172B GLU* 3.7 48.0 - - + +
2175B LEU* 4.4 2.7 - - + -
2184B VAL* 3.9 26.7 + - + +
2185B THR* 1.3 75.2 - - - +
2187B MSE 1.3 63.3 + - - +
2188B GLU 4.2 1.2 + - - -
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Residues in contact with MSE2187 (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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2159B TYR* 3.6 21.5 - - + -
2160B ALA 2.8 9.6 + - - +
2161B ILE* 3.2 55.8 - - + +
2162B ASP 3.4 4.2 + - - -
2168B ILE* 3.5 4.4 - - - +
2185B THR* 3.9 18.2 - - + +
2186B LEU* 1.3 81.6 - - - +
2188B GLU* 1.3 63.7 + - - +
2194B ALA* 4.2 19.3 - - + +
2197B LYS* 5.7 5.8 - - - -
2198B ILE* 3.1 42.2 - - + -
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Residues in contact with GLU2188 (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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2162B ASP 3.5 10.8 - - - +
2163B ARG 4.2 5.4 - - - +
2165B PRO* 3.5 37.2 - - + +
2168B ILE* 3.7 24.7 - - + +
2186B LEU 4.2 1.0 + - - -
2187B MSE 1.3 74.9 - - - +
2189B GLY* 1.3 62.8 + - - +
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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