Contacts of the strand formed by residues 1238 - 1243 (chain B) in PDB entry 1FO4
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 GLU1238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B PRO 5.2 2.0 - - - +
555B ALA* 3.1 29.7 - - + +
1174B LEU 3.1 9.5 + - - +
1175B ARG* 3.2 43.2 + - + +
1176B THR 2.9 29.0 + - - +
1236B PRO* 3.7 3.3 - - - +
1237B THR* 1.3 82.4 - - + +
1239B PHE* 1.3 58.2 + - - +
1240B ARG* 4.1 12.0 + - + -
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Residues in contact with PHE1239 (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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152B GLY 4.5 3.1 - - - -
154B ARG* 3.9 24.0 - - + -
555B ALA 3.0 7.7 + - - -
556B ASN* 3.3 35.8 + - - +
557B ILE 3.3 3.3 + - - +
558B GLN* 4.7 1.9 + - - -
1176B THR* 3.7 9.0 - - + -
1178B ILE* 4.0 22.4 - - + -
1196B GLU* 4.0 35.2 - - + -
1199B PHE* 3.8 23.8 - + + -
1200B VAL* 4.4 13.0 - - + -
1235B ILE* 4.6 5.6 - - + -
1236B PRO* 3.6 34.1 - - + +
1238B GLU* 1.3 72.9 - - - +
1240B ARG* 1.3 65.3 + - - +
1241B VAL* 4.1 10.6 + - + +
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Residues in contact with ARG1240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ALA* 5.0 5.6 + - - +
557B ILE* 3.2 40.4 - - + +
974B SER* 3.5 13.9 + - - +
976B GLN* 5.7 0.8 + - - -
1175B ARG* 3.1 31.8 - - - +
1176B THR 3.0 9.7 + - - +
1177B ASP* 3.1 26.6 - - + +
1178B ILE* 2.9 26.9 + - - +
1238B GLU* 4.6 11.0 + - + -
1239B PHE* 1.3 79.7 - - - +
1241B VAL* 1.3 66.7 + - - +
1242B SER* 5.2 2.9 - - - +
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Residues in contact with VAL1241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ILE 3.0 8.3 + - - +
558B GLN* 3.2 6.6 - - + +
559B LEU 2.8 23.7 + - - +
1178B ILE* 3.5 9.0 - - + +
1180B MET* 5.6 0.4 - - + -
1192B ILE* 4.3 26.6 - - + +
1195B VAL* 3.7 33.4 - - + -
1196B GLU* 3.8 32.3 - - + +
1239B PHE* 4.1 15.0 - - + +
1240B ARG* 1.3 79.7 - - - +
1242B SER* 1.3 71.0 + - - +
1243B LEU* 4.9 1.1 - - + -
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Residues in contact with SER1242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LEU* 3.2 33.8 - - - +
970B GLU* 5.1 6.1 - - - -
974B SER* 5.4 5.0 + - - -
1178B ILE 2.8 15.2 + - - -
1179B VAL* 3.4 15.7 - - - +
1180B MET* 2.9 26.9 + - - +
1240B ARG* 5.2 2.6 - - - +
1241B VAL* 1.3 80.4 + - - +
1243B LEU* 1.3 68.9 + - - +
1244B LEU 3.7 0.4 + - - -
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Residues in contact with LEU1243 (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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559B LEU 2.8 14.2 + - - +
560B PHE* 4.2 11.8 - - + -
561B GLN 5.0 2.4 + - - +
1180B MET* 3.4 16.6 - - + +
1182B VAL* 3.9 33.7 - - + -
1183B GLY 5.9 0.7 - - - +
1185B SER* 4.1 7.2 - - - +
1188B PRO* 3.9 28.7 - - + -
1191B ASP* 4.3 2.9 - - + -
1192B ILE* 3.7 36.8 - - + +
1195B VAL* 4.7 7.0 - - + -
1241B VAL* 4.9 1.6 - - + -
1242B SER* 1.3 80.4 - - - +
1244B LEU* 1.3 69.4 + - - +
1245B ARG* 3.2 11.1 + - - +
4008B GOL 5.9 0.2 - - - +
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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
------------------------------------------------------------
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