Contacts of the strand formed by residues 936 - 947 (chain B) in PDB entry 5FO9
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 ILE 936 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935B GLY* 1.3 75.0 - - - +
937B ARG* 1.3 75.6 + - + +
938B MET* 3.4 16.9 + - + -
1349B HIS* 4.4 7.3 + - - -
1350B ALA* 2.8 41.7 + - + +
1352B ALA* 4.4 16.2 - - + -
1355B GLN* 4.7 23.6 - - - +
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Residues in contact with ARG 937 (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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141A PRO* 4.6 10.1 - - - +
197A GLU 2.8 28.3 + - - -
198A LEU* 4.2 18.8 - - + +
199A VAL* 2.4 37.7 + - - +
201A MET* 3.9 21.3 - - - +
226A GLU* 4.9 6.8 + - - -
936B ILE* 1.3 81.7 - - + +
938B MET* 1.3 76.2 + - - +
1347B MET* 6.1 6.7 - - + -
1348B TYR 3.5 11.7 - - - +
1349B HIS* 4.4 17.1 + - + -
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Residues in contact with MET 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936B ILE* 3.4 17.9 + - + +
937B ARG* 1.3 88.4 - - - +
939B ASN* 1.3 67.5 + - - +
940B LYS 3.9 0.4 - - - -
969B ASP* 5.6 0.2 - - - +
1347B MET* 3.9 2.4 - - - -
1348B TYR* 3.2 56.4 + - + +
1350B ALA* 3.6 24.9 - - + -
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Residues in contact with ASN 939 (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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938B MET* 1.3 77.7 - - - +
940B LYS* 1.3 60.8 - - - +
941B THR* 3.7 5.2 + - - -
1345B VAL* 4.4 14.3 - - + +
1346B THR 3.5 11.0 - - - +
1347B MET* 4.7 13.2 - - + +
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Residues in contact with LYS 940 (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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938B MET 3.7 3.0 + - - -
939B ASN* 1.3 70.3 - - - +
941B THR* 1.3 70.9 + - - +
942B VAL* 3.3 4.4 + - + +
965B ALA* 4.9 6.7 - - + -
966B ASP* 3.6 45.6 + - + +
967B LEU 4.3 6.4 - - - +
968B SER* 5.0 1.6 + - - -
969B ASP* 4.5 6.3 + - - -
1345B VAL* 4.6 0.7 - - - -
1346B THR* 3.2 33.1 + - - +
1348B TYR* 3.9 32.0 + - + -
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Residues in contact with THR 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B ASN* 3.7 4.9 + - - +
940B LYS* 1.3 77.1 - - - +
942B VAL* 1.3 65.5 + - - +
943B ALA 4.4 10.8 - - - +
944B VAL* 5.0 11.9 - - + -
1344B VAL 4.2 2.5 - - - +
1345B VAL* 3.7 29.4 - - + +
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Residues in contact with VAL 942 (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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940B LYS* 3.3 6.0 + - + +
941B THR* 1.3 75.6 - - - +
943B ALA* 1.3 69.8 + - + +
945B ARG* 5.5 0.2 + - - -
962B ILE* 4.1 3.4 - - + -
963B PRO* 3.6 29.4 - - + +
964B PRO 5.0 2.5 - - - +
965B ALA* 3.8 21.3 - - + +
1344B VAL* 2.8 31.2 + - + +
1346B THR* 3.7 31.0 - - + +
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Residues in contact with ALA 943 (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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941B THR* 3.9 3.9 - - - +
942B VAL* 1.3 89.5 - - + +
944B VAL* 1.3 63.8 + - - +
945B ARG* 3.7 37.7 - - + +
962B ILE* 4.7 9.2 - - + -
963B PRO* 5.5 0.2 - - + -
1342B LEU* 3.7 1.0 - - - +
1343B SER* 3.4 4.3 - - - -
1344B VAL* 2.9 41.4 + - + +
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Residues in contact with VAL 944 (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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941B THR* 5.0 12.8 - - + -
943B ALA* 1.3 76.3 - - - +
945B ARG* 1.3 69.4 + - - +
946B THR 4.4 0.2 + - - -
1341B THR* 5.9 4.7 - - + -
1342B LEU 3.4 3.8 - - - +
1343B SER* 4.3 17.3 - - - -
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Residues in contact with ARG 945 (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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943B ALA* 3.7 30.6 - - + +
944B VAL* 1.3 81.7 + - - +
946B THR* 1.3 63.0 + - - +
947B LEU* 3.7 6.0 + - + +
960B GLU* 3.8 29.0 + - + +
961B ASP 3.1 29.5 + - - +
962B ILE* 4.4 6.6 - - + +
963B PRO* 4.2 12.3 - - - +
1341B THR* 3.9 2.8 - - - +
1342B LEU* 2.9 59.4 + - + +
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Residues in contact with THR 946 (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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944B VAL 4.4 0.4 + - - -
945B ARG* 1.3 72.9 - - - +
947B LEU* 1.3 67.5 + - - +
948B ASP* 5.6 1.6 - - + -
951B ARG* 5.1 12.3 - - - +
952B LEU* 3.7 14.6 - - + +
958B GLN* 3.3 15.9 + - - -
960B GLU* 4.6 0.7 - - - +
1339B GLN* 5.8 4.5 - - + -
1340B GLY 3.8 11.4 - - - +
1341B THR* 4.8 8.2 + - - +
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Residues in contact with LEU 947 (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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945B ARG* 4.1 14.6 - - + +
946B THR* 1.3 77.1 - - - +
948B ASP* 1.3 62.7 + - - +
949B PRO* 3.8 3.6 - - + +
958B GLN* 3.3 24.0 - - + +
960B GLU* 3.7 22.2 - - + -
982B LEU* 4.5 11.4 - - + -
1294B LEU* 5.8 3.1 - - + -
1296B VAL* 4.7 6.5 - - + -
1332B VAL* 4.3 14.6 - - + -
1334B ALA* 4.0 23.1 - - + -
1338B GLY 3.9 1.0 - - - +
1339B GLN* 3.6 4.2 - - - +
1340B GLY* 2.9 49.4 + - - +
1341B THR 5.4 0.2 - - - -
1342B LEU* 4.2 19.7 - - + +
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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