Contacts of the strand formed by residues 994 - 1007 (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 LYS 994 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B LYS* 4.2 7.5 - - - +
544B SER* 3.1 47.3 + - - +
545B ALA* 4.3 2.2 - - - +
547B LEU* 4.4 10.5 + - - -
987B PHE* 3.6 17.2 - - + -
991B ASN* 3.3 18.8 - - + +
992B CYS 3.7 0.4 - - - -
993B TRP* 1.3 81.5 + - + +
995B LYS* 1.3 74.5 + - - +
1163B GLU* 3.7 21.8 - - + +
1164B ILE 3.3 13.7 - - - +
1165B ASP* 3.5 27.8 + - - +
1166B CYS* 3.9 1.1 - - - -
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Residues in contact with LYS 995 (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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987B PHE* 4.0 2.0 - - - -
988B ASN* 2.9 33.6 + - - +
991B ASN 2.8 18.7 + - - +
992B CYS 4.1 5.6 - - - -
994B LYS* 1.3 79.7 - - - +
996B ARG* 1.3 64.7 + - - +
1163B GLU* 3.2 2.5 - - - +
1164B ILE* 2.8 47.2 + - + +
1166B CYS* 3.6 15.2 - - - -
1277B ALA* 3.7 18.4 - - - +
1280B ALA* 3.9 11.5 + - + +
1281B ALA* 3.9 12.8 - - - +
1284B GLN* 2.8 51.3 - - - +
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Residues in contact with ARG 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B HIS* 5.3 6.5 + - - -
983B GLU* 2.9 33.8 + - - -
984B VAL* 3.4 21.9 - - + +
987B PHE* 3.4 36.3 - - + -
988B ASN* 2.7 26.7 + - - +
995B LYS* 1.3 74.9 - - - +
997B GLY* 1.3 59.4 + - - +
1161B GLU* 3.7 9.3 + - - +
1162B VAL 3.1 12.8 - - - +
1163B GLU* 2.7 31.8 + - + -
1174B LEU* 3.5 25.7 - - - +
1276B ASP* 4.7 2.1 - - - +
1277B ALA* 3.8 10.6 - - - -
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Residues in contact with GLY 997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984B VAL* 4.5 3.1 - - - -
996B ARG* 1.3 74.5 - - - +
998B LEU* 1.3 59.2 + - - -
1161B GLU* 3.1 9.4 - - - +
1162B VAL* 2.9 30.6 + - - +
1273B ALA* 3.3 26.0 - - - -
1276B ASP* 3.6 9.4 - - - -
1277B ALA* 3.9 7.0 - - - +
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Residues in contact with LEU 998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977B TYR* 3.8 34.3 + - + +
980B ARG* 3.7 22.7 - - + +
981B LYS* 3.8 38.1 - - + +
984B VAL* 4.3 11.0 - - + -
997B GLY* 1.3 74.5 - - - +
999B CYS* 1.3 65.5 + - - +
1159B CYS* 3.5 28.0 - - - -
1160B SER 3.4 12.6 - - - +
1161B GLU* 4.0 9.6 - - + -
1273B ALA* 4.1 2.6 + - - -
1276B ASP* 3.1 22.3 + - - +
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Residues in contact with CYS 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B ALA* 5.7 2.7 - - - -
942B ARG* 3.9 15.9 - - - -
977B TYR* 4.6 4.7 - - - -
998B LEU* 1.3 81.5 - - - +
1000B ILE* 1.3 63.9 + - - +
1001B ILE* 3.7 21.5 - - - -
1158B ALA 3.8 1.6 - - - +
1159B CYS* 3.5 3.5 - - - -
1160B SER 3.1 30.1 + - - +
1269B SER* 4.0 7.9 - - - +
1272B PHE* 3.6 25.8 - - - +
1273B ALA* 3.8 20.0 - - - +
1276B ASP* 5.4 0.2 - - + -
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Residues in contact with ILE1000 (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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939B GLU* 4.0 15.0 - - + -
942B ARG* 3.8 8.5 + - - -
968B TRP* 3.6 34.1 - - + +
971B CYS* 4.2 13.9 - - + -
972B LEU* 3.6 32.1 - - + +
977B TYR* 3.8 23.5 + - + +
999B CYS* 1.3 76.8 - - - +
1001B ILE* 1.3 67.5 + - - +
1157B VAL* 3.4 31.6 - - + -
1158B ALA 3.3 7.0 - - - +
1159B CYS* 4.1 9.0 - - + +
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Residues in contact with ILE1001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B GLU* 3.8 11.7 - - + +
942B ARG* 3.6 37.5 - - - +
999B CYS* 3.7 15.5 - - - -
1000B ILE* 1.3 74.4 - - - +
1002B PRO* 1.3 80.1 - - + +
1157B VAL* 3.3 5.1 - - - -
1158B ALA 2.9 33.9 + - - +
1265B PHE* 3.7 27.8 - - + +
1266B LEU* 3.6 7.4 - - + +
1268B ALA* 4.5 3.1 - - + +
1269B SER* 3.8 30.7 - - - +
1272B PHE* 4.2 7.6 - - + -
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Residues in contact with PRO1002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B ASN* 3.3 13.9 + - - +
888B CYS* 4.1 7.9 - - + -
889B TYR* 3.4 31.9 - - + +
924B GLU* 3.8 0.7 - - - +
942B ARG* 4.1 3.8 - - - -
946B MET* 4.2 4.5 - - + -
964B VAL* 3.9 25.1 - - + -
968B TRP* 3.8 23.3 - - + -
1001B ILE* 1.3 101.4 - - + +
1003B THR* 1.3 66.2 + - - +
1156B GLY 3.5 7.6 - - - +
1157B VAL* 4.0 2.9 - - + -
1265B PHE* 4.2 0.7 - - - -
1266B LEU* 4.3 0.4 - - - -
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Residues in contact with THR1003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B ASN* 3.4 8.3 + - - -
888B CYS* 3.5 8.2 - - - -
920B LEU* 3.6 24.6 - - - +
964B VAL* 4.1 1.2 - - - +
1002B PRO* 1.3 78.9 - - - +
1004B LYS* 1.3 69.0 + - - +
1005B PHE* 5.6 0.5 - - - +
1154B THR 5.3 0.9 - - - +
1155B TYR* 3.4 5.8 - - - +
1156B GLY* 2.9 37.6 + - - +
1180B MET* 4.7 3.4 - - + -
1262B PRO* 3.8 21.7 + - + +
1265B PHE* 3.7 10.8 - - - +
1266B LEU* 3.7 21.5 - - + +
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Residues in contact with LYS1004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883B PHE 4.4 6.7 + - - -
884B HIS* 3.5 17.7 - - + +
886B ASP* 2.8 28.3 + - - -
887B ASN* 2.8 35.7 + - - +
888B CYS* 3.9 5.6 - - - -
920B LEU* 4.5 7.6 - - - +
947B TYR* 4.2 3.4 - - + -
953B THR* 4.2 6.8 - - - +
955B PHE* 5.1 0.2 - - - -
959B LEU* 4.1 17.3 - - + -
962B PHE* 4.4 8.7 - - + -
1003B THR* 1.3 82.9 + - - +
1005B PHE* 1.3 60.5 + - - +
1153B PHE* 3.9 29.9 - - + -
1154B THR 3.3 6.5 - - - -
1155B TYR* 3.5 28.7 - - + -
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Residues in contact with PHE1005 (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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880B ARG* 3.5 28.9 - - - -
884B HIS* 3.7 10.5 - + - -
913B GLY* 3.4 33.0 - - - -
916B GLY* 4.6 7.4 - - - -
917B PRO* 5.1 1.3 - - + -
920B LEU* 5.0 9.4 - - + -
1003B THR* 5.6 0.9 - - + +
1004B LYS* 1.3 75.6 - - - +
1006B GLY* 1.3 82.4 + - - +
1007B ILE* 3.5 10.0 + - + +
1079B ALA 5.2 2.0 - - - -
1080B SER* 4.7 0.7 - - - -
1153B PHE* 3.4 5.1 - - - -
1154B THR 3.0 28.3 + - - +
1261B GLU* 3.6 38.1 - - + -
1262B PRO* 3.7 45.3 - - + +
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Residues in contact with GLY1006 (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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880B ARG* 2.8 24.6 + - - -
884B HIS* 3.0 14.1 + - - -
1005B PHE* 1.3 79.1 - - - +
1007B ILE* 1.3 58.9 + - - +
1079B ALA 5.6 0.2 - - - +
1150B PHE* 3.3 32.5 - - - -
1153B PHE* 3.5 17.5 - - - -
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Residues in contact with ILE1007 (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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1005B PHE* 3.6 30.3 - - + +
1006B GLY* 1.3 77.0 - - - +
1008B SER* 1.3 73.4 + - - +
1079B ALA 4.8 1.1 - - - +
1080B SER* 4.7 4.3 - - - -
1081B VAL* 3.4 24.5 - - + -
1084B ASP* 4.0 2.2 - - - +
1150B PHE* 3.5 3.2 - - - +
1151B HIS* 3.0 20.3 + - + +
1152B TYR* 2.9 55.1 + - + +
1154B THR* 3.6 19.1 - - - +
1258B ALA* 3.6 20.6 - - + -
1262B PRO* 4.0 4.7 - - + -
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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
------------------------------------------------------------
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