Contacts of the strand formed by residues 2224 - 2234 (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 LEU2224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2201B ILE* 3.6 24.9 - - + +
2202B ASP 4.1 2.7 - - - +
2203B ILE 4.7 0.2 - - - +
2204B ALA* 4.9 0.7 - - + -
2220B ILE* 3.1 14.0 + - + +
2221B LYS* 3.0 13.3 + - - +
2222B ASP 3.5 0.4 - - - -
2223B LYS* 1.3 77.8 - - - +
2225B LYS* 1.3 66.8 + - - +
2226B PRO* 3.7 3.6 - - - +
2228B GLY* 3.7 35.2 - - - +
2229B ARG 3.9 15.5 - - - +
2230B ILE* 4.0 23.1 - - + -
2252B PHE* 4.0 22.4 - - + -
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Residues in contact with LYS2225 (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 5.4 0.2 + - - -
2136B VAL* 4.2 16.2 - - - +
2156B ARG* 4.6 9.5 - - - +
2200B ASP* 3.7 37.4 + - + +
2201B ILE 2.8 18.0 + - - +
2202B ASP* 3.1 39.5 + - - +
2223B LYS 3.3 0.4 + - - -
2224B LEU* 1.3 77.6 - - - +
2226B PRO* 1.3 73.1 - - + +
2228B GLY* 2.8 23.7 + - - -
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Residues in contact with PRO2226 (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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2202B ASP* 5.1 2.6 - - - +
2224B LEU 4.1 3.8 - - - +
2225B LYS* 1.3 91.7 - - + +
2227B GLY* 1.3 59.5 + - - +
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Residues in contact with GLY2227 (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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2202B ASP* 6.0 0.2 - - - -
2226B PRO* 1.3 73.5 - - - +
2228B GLY* 1.3 61.7 + - - +
2229B ARG* 2.9 30.5 + - - +
2286B VAL* 4.8 18.4 - - - +
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Residues in contact with GLY2228 (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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2202B ASP* 3.0 18.8 + - - -
2224B LEU* 3.7 22.7 - - - +
2225B LYS* 2.8 17.8 + - - -
2226B PRO 3.2 0.2 - - - -
2227B GLY* 1.3 83.6 - - - +
2229B ARG* 1.3 62.4 + - - +
2252B PHE* 5.7 0.5 - - - -
2284B THR* 4.5 1.2 + - - -
2285B GLY 4.0 11.3 - - - +
2286B VAL* 4.8 1.4 - - - -
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Residues in contact with ARG2229 (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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2128B LEU 4.1 7.6 - - - +
2129B ALA* 2.7 43.5 + - - +
2130B GLU* 2.8 34.8 + - - +
2135B ASP* 3.8 20.2 + - - -
2202B ASP* 2.8 26.8 + - - +
2203B ILE* 3.4 13.6 - - + +
2204B ALA* 2.8 26.3 + - - +
2224B LEU* 3.9 1.8 - - - +
2227B GLY 2.9 26.9 + - - +
2228B GLY* 1.3 75.9 - - - +
2230B ILE* 1.3 67.7 + - - +
2231B ILE* 5.1 5.2 - - + -
2284B THR* 4.1 7.2 - - - +
2285B GLY 4.9 1.1 - - - +
2286B VAL* 3.6 25.7 - - + +
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Residues in contact with ILE2230 (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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2204B ALA* 3.2 12.1 - - + +
2206B VAL* 4.9 2.9 - - + -
2217B LEU* 4.2 24.5 - - + +
2220B ILE* 3.7 27.4 - - + -
2221B LYS 4.9 3.6 - - - +
2224B LEU* 4.0 14.1 - - + -
2229B ARG* 1.3 78.3 - - - +
2231B ILE* 1.3 71.8 + - - +
2232B VAL* 4.2 10.3 - - + -
2247B LEU* 4.3 12.3 - - + -
2252B PHE* 3.8 32.5 - - + -
2282B ILE 4.6 0.2 - - - -
2283B TYR* 3.4 2.1 - - - +
2284B THR* 3.2 37.2 + - + +
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Residues in contact with ILE2231 (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* 3.6 40.2 - - + +
2128B LEU* 3.7 12.1 - - + -
2129B ALA* 3.6 25.4 - - + +
2203B ILE* 5.4 1.3 - - + -
2204B ALA 2.8 11.6 + - - +
2205B VAL* 3.2 15.7 - - + +
2206B VAL 2.8 24.9 + - - -
2229B ARG* 5.1 5.8 - - + -
2230B ILE* 1.3 82.0 - - - +
2232B VAL* 1.3 69.1 + - - +
2233B THR* 5.1 0.4 - - - +
2281B LEU* 4.5 24.7 - - + -
2282B ILE 3.5 6.3 - - - +
2283B TYR* 4.1 13.0 - - + -
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Residues in contact with VAL2232 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2206B VAL* 3.4 19.3 - - + +
2207B GLY 5.3 0.9 - - - +
2209B SER* 5.8 0.2 - - - -
2213B LEU* 4.4 11.2 - - + -
2217B LEU* 4.0 26.2 - - + -
2230B ILE* 4.3 7.9 - - + -
2231B ILE* 1.3 77.7 - - - +
2233B THR* 1.3 72.5 + - - +
2234B ALA 3.8 0.7 + - - -
2239B THR* 4.5 9.9 - - + -
2243B ALA* 4.3 17.3 - - + -
2247B LEU* 4.4 11.7 - - + -
2280B ALA 3.7 0.2 - - - +
2281B LEU* 3.3 6.6 - - - -
2282B ILE* 2.8 49.2 + - + +
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Residues in contact with THR2233 (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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2117B THR* 5.2 10.7 - - + +
2121B VAL* 5.1 0.9 - - - +
2125B ILE* 3.9 15.6 - - - +
2147B VAL* 5.9 0.3 - - - +
2205B VAL* 4.7 5.7 - - - +
2206B VAL 2.8 15.6 + - - +
2207B GLY* 3.7 29.3 - - - +
2231B ILE* 4.0 0.7 + - - +
2232B VAL* 1.3 76.5 - - - +
2234B ALA* 1.3 64.5 + - - +
2235B ILE* 4.2 10.1 + - + +
2239B THR* 4.4 3.6 - - - +
2279B VAL* 4.5 14.6 - - + -
2280B ALA 3.6 4.7 - - - -
2281B LEU* 3.8 14.6 - - - +
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Residues in contact with ALA2234 (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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2232B VAL 3.8 0.6 + - - -
2233B THR* 1.3 76.0 - - - +
2235B ILE* 1.3 69.2 + - - +
2239B THR* 3.8 24.5 - - + -
2240B LYS* 3.7 29.2 - - + -
2279B VAL* 3.7 1.4 - - - +
2280B ALA* 2.9 36.6 + - + +
2282B ILE* 3.9 15.9 - - + -
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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