Contacts of the strand formed by residues 2201 - 2206 (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 ILE2201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2136B VAL* 3.3 20.6 - - + +
2137B ALA 4.4 0.4 - - - -
2138B VAL* 3.6 39.3 - - + +
2195B LEU* 5.8 2.0 - - + -
2198B ILE* 4.3 8.1 - - + -
2199B PRO 4.2 6.5 - - - +
2200B ASP* 1.3 82.0 - - - +
2202B ASP* 1.3 62.7 + - - +
2203B ILE 3.9 5.8 - - - +
2204B ALA* 4.0 12.8 - - + -
2220B ILE* 4.0 18.8 - - + -
2223B LYS* 2.8 25.1 + - + +
2224B LEU* 3.6 11.7 - - + +
2225B LYS* 2.8 27.9 + - - -
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Residues in contact with ASP2202 (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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2134B ASN 4.3 2.3 - - - +
2135B ASP* 3.2 36.1 - - + +
2136B VAL* 2.7 27.3 + - - +
2201B ILE* 1.3 73.8 - - - +
2203B ILE* 1.3 63.6 + - - +
2224B LEU* 4.3 1.3 - - - -
2225B LYS* 3.1 40.7 + - - +
2226B PRO 5.1 2.9 - - - +
2227B GLY 6.0 0.2 - - - -
2228B GLY* 3.0 11.4 - - - -
2229B ARG* 2.8 34.0 + - - +
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Residues in contact with ILE2203 (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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2129B ALA* 3.7 37.9 - - + +
2131B PRO* 3.9 20.6 - - + -
2135B ASP* 4.0 15.5 - - + +
2136B VAL 3.4 2.3 + - - +
2137B ALA* 3.1 17.0 - - + -
2138B VAL* 3.1 24.9 + - - +
2151B LEU* 4.6 7.2 - - + -
2155B VAL* 4.3 8.7 - - + -
2201B ILE* 3.9 4.1 - - - +
2202B ASP* 1.3 88.5 - - + +
2204B ALA* 1.3 64.7 + - - +
2205B VAL* 4.3 16.2 - - + -
2229B ARG* 3.4 26.2 - - + +
2231B ILE* 5.4 0.9 - - + -
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Residues in contact with ALA2204 (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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2138B VAL* 3.6 18.4 - - + -
2201B ILE* 4.0 4.0 - - + -
2203B ILE* 1.3 76.1 - - - +
2205B VAL* 1.3 63.2 + - - +
2206B VAL 4.1 0.4 - - - -
2220B ILE* 3.6 38.4 - - + -
2224B LEU* 4.9 0.7 - - + -
2229B ARG 2.8 13.6 + - - +
2230B ILE* 3.2 7.6 - - + +
2231B ILE* 2.8 26.3 + - - +
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Residues in contact with VAL2205 (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 ILE* 4.0 32.1 - - + -
2129B ALA* 5.4 0.9 - - + -
2138B VAL 3.1 8.1 + - - +
2139B ASP* 3.4 18.4 - - - +
2140B VAL* 2.8 32.9 + - - +
2147B VAL* 4.2 22.7 - - + -
2151B LEU* 4.6 7.6 - - + -
2203B ILE* 4.3 16.4 - - + -
2204B ALA* 1.3 77.2 - - - +
2206B VAL* 1.3 66.2 + - - +
2207B GLY* 4.8 1.1 - - - +
2231B ILE* 3.2 17.7 - - + +
2233B THR* 4.7 5.6 - - - +
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Residues in contact with VAL2206 (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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2140B VAL* 3.7 16.8 - - + +
2205B VAL* 1.3 80.0 - - - +
2207B GLY* 1.3 68.5 + - - +
2209B SER* 4.4 10.8 - - - -
2213B LEU* 4.1 22.9 - - + -
2216B ILE* 4.2 7.2 - - + -
2217B LEU* 4.2 13.7 - - + -
2220B ILE* 3.6 30.5 - - + -
2230B ILE* 4.9 3.6 - - + -
2231B ILE 2.8 12.7 + - - +
2232B VAL* 3.4 12.2 - - + +
2233B THR* 2.8 27.4 + - - -
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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