Contacts of the helix formed by residues 978 - 994 (chain B) in PDB entry 5IYB
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 978 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ILE* 5.6 0.4 - - + -
692A SER* 5.0 7.2 - - - +
766A PHE* 5.7 2.7 - - + -
784A VAL* 3.4 37.5 - - + -
827A TYR* 3.7 23.1 - - + +
828A LEU* 4.0 14.6 - - + -
716B HIS* 3.0 10.7 + - + +
972B ILE* 4.9 8.1 - - + +
976B MET* 3.5 23.8 - - + +
977B THR* 1.3 71.0 - - - +
979B GLY* 1.3 58.4 + - - +
980B HIS 3.1 2.0 - - - -
981B LEU* 2.7 41.0 + - + +
982B ILE* 3.1 28.8 + - + +
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Residues in contact with GLY 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B PHE* 4.4 10.2 - - - -
716B HIS* 3.1 26.8 + - - +
717B ASN* 4.1 4.9 - - - -
939B HIS* 3.3 18.1 - - - -
977B THR 3.2 0.6 - - - -
978B ILE* 1.3 78.4 - - - +
980B HIS* 1.3 55.1 + - - +
982B ILE* 3.2 6.1 + - - -
983B GLU* 2.8 29.1 + - - +
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Residues in contact with HIS 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B VAL* 5.0 5.2 - - + -
782B ILE* 4.7 19.1 - - + -
937B SER* 3.8 16.4 + - - -
939B HIS* 3.1 24.7 + + + -
941B GLN* 3.6 33.0 - - + +
967B ILE* 4.5 11.2 - - + +
972B ILE* 4.3 10.7 - - + +
977B THR* 3.3 23.8 + - - +
978B ILE 3.1 0.6 - - - -
979B GLY* 1.3 77.5 - - - +
981B LEU* 1.3 64.2 + - + +
983B GLU* 3.9 2.1 - - - +
984B CYS* 3.3 18.4 + - + +
1046B THR* 4.2 22.8 + - + +
1048B TYR* 4.3 11.0 + + - -
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Residues in contact with LEU 981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ILE* 4.0 15.0 - - + +
688A GLY 3.5 26.5 - - - +
689A ILE* 3.4 22.0 - - + +
692A SER* 5.1 2.5 - - - +
782B ILE* 4.5 7.2 - - + -
972B ILE* 4.2 34.3 - - + -
977B THR 4.4 6.3 - - - +
978B ILE* 2.7 27.9 + - + +
980B HIS* 1.3 79.5 - - - +
982B ILE* 1.3 54.5 + - + +
984B CYS* 3.1 4.2 - - - +
985B LEU* 2.9 26.2 + - - +
1042B PHE* 3.6 27.9 - - + -
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Residues in contact with ILE 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ILE* 3.8 24.2 - - + -
828A LEU* 4.4 11.0 - - + -
713B PHE* 3.5 28.7 - - + -
716B HIS* 4.2 11.4 - - + -
978B ILE* 3.2 31.4 - - + +
979B GLY* 3.7 7.0 - - - +
981B LEU* 1.3 70.1 - - - +
983B GLU* 1.3 66.1 + - - +
984B CYS 3.2 1.1 - - - -
985B LEU* 4.0 7.6 - - + +
986B GLN* 3.0 26.0 + - - +
1007B ASN* 3.4 29.2 - - + +
1008B VAL* 5.1 4.7 - - + -
1011B ILE* 4.7 6.5 - - + +
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Residues in contact with GLU 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B PRO* 3.1 19.6 - - + +
713B PHE* 3.7 12.4 - - + -
759B VAL* 3.4 15.2 - - + +
938B ARG* 3.0 35.2 + - - +
939B HIS* 2.6 33.6 + - - +
979B GLY 2.8 20.2 + - - +
980B HIS 3.9 2.0 - - - +
982B ILE* 1.3 73.1 - - - +
984B CYS* 1.3 53.4 + - - +
986B GLN* 3.4 0.6 + - - +
987B GLY* 2.9 28.6 + - - -
1045B PRO 4.6 0.4 - - - +
1046B THR* 3.3 27.0 - - + +
1047B TYR* 3.3 12.1 + - - +
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Residues in contact with CYS 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B VAL* 4.8 3.8 - - - -
782B ILE* 5.1 6.1 - - - -
980B HIS* 3.3 14.8 + - - +
981B LEU* 3.1 11.7 - - - +
983B GLU* 1.3 78.4 - - - +
985B LEU* 1.3 58.6 + - - +
987B GLY 3.5 0.2 + - - -
988B LYS* 3.1 26.2 + - - +
1042B PHE* 3.7 23.6 - - + -
1043B ILE 4.8 0.9 - - - -
1044B GLY* 3.8 24.4 - - - -
1045B PRO 3.4 21.5 - - - +
1046B THR* 3.6 17.0 - - - +
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Residues in contact with LEU 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ILE* 3.5 27.4 - - + -
981B LEU 2.9 19.1 + - - +
982B ILE* 3.5 9.2 + - + +
984B CYS* 1.3 71.8 - - - +
986B GLN* 1.3 61.7 + - - +
988B LYS* 3.3 19.5 - - + +
989B VAL* 3.4 12.5 + - - +
1007B ASN 5.5 0.7 - - - +
1008B VAL* 5.1 2.0 - - - +
1011B ILE* 4.2 22.4 - - + -
1012B SER* 3.9 13.9 - - - +
1015B LEU* 3.8 17.0 - - + +
1022B LEU 4.6 1.8 - - - +
1023B ARG* 3.7 30.7 - - - +
1024B GLY* 3.7 9.4 - - - +
1042B PHE* 4.0 11.0 - - + -
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Residues in contact with GLN 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B PHE* 4.0 15.4 - - + -
759B VAL* 3.6 25.6 - - + -
982B ILE 3.0 19.6 + - - +
983B GLU 3.5 4.0 - - - +
985B LEU* 1.3 76.1 - - - +
987B GLY* 1.3 57.4 + - - +
989B VAL* 3.3 17.5 + - - +
990B SER* 3.0 27.5 + - - -
997B GLY* 4.1 6.2 - - - -
998B ASP 4.4 12.4 + - - +
1011B ILE* 3.2 32.9 - - + +
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Residues in contact with GLY 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B LEU* 3.9 7.9 - - - +
759B VAL* 3.4 19.0 - - - +
983B GLU 2.9 12.8 + - - -
984B CYS 3.5 2.9 + - - -
985B LEU 3.4 0.2 - - - -
986B GLN* 1.3 77.4 - - - +
988B LYS* 1.3 55.9 + - - +
990B SER* 3.6 5.9 - - - -
991B ALA* 3.0 22.3 + - - +
1045B PRO* 3.5 22.1 - - - +
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Residues in contact with LYS 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984B CYS 3.1 13.3 + - - +
985B LEU* 3.3 14.8 - - + +
987B GLY* 1.3 73.5 - - - +
989B VAL* 1.3 62.1 + - - +
991B ALA* 3.6 2.8 + - - +
992B ASN* 3.0 34.5 + - - +
1015B LEU* 3.6 27.8 - - + -
1020B TYR* 4.1 16.5 - - + -
1024B GLY* 3.8 15.9 - - - -
1026B GLU* 2.2 33.2 + - - -
1042B PHE* 6.2 0.4 - - + -
1043B ILE 3.2 18.8 + - - +
1044B GLY* 4.2 2.1 - - - -
1045B PRO* 4.0 13.4 - - + +
43J TYR* 3.5 24.0 + - + +
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Residues in contact with VAL 989 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985B LEU 3.4 5.8 + - - +
986B GLN* 3.3 18.7 + - - +
988B LYS* 1.3 74.6 - - - +
990B SER* 1.3 60.6 + - - +
992B ASN* 3.4 3.8 + - - +
993B LYS* 2.9 38.3 + - + +
1011B ILE* 3.5 32.8 - - + +
1014B LEU* 4.5 19.7 - - + -
1015B LEU* 3.9 29.8 - - + +
1018B TYR* 4.6 12.1 - - + -
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Residues in contact with SER 990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B LEU* 4.0 19.4 + - - -
759B VAL* 4.7 0.7 - - - +
986B GLN* 3.0 14.7 + - - -
987B GLY* 3.6 10.2 - - - -
988B LYS 3.3 0.2 - - - -
989B VAL* 1.3 77.9 - - - +
991B ALA* 1.3 55.6 + - - +
993B LYS* 4.7 0.9 - - - -
994B GLY* 2.7 30.8 + - - -
995B GLU 3.2 18.3 + - - +
996B ILE* 4.4 0.4 - - - -
997B GLY* 2.9 33.6 + - - -
50J LEU* 3.8 4.0 - - - +
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Residues in contact with ALA 991 (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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758B LEU* 4.6 8.2 - - + +
987B GLY 3.0 16.2 + - - +
988B LYS 3.9 4.7 - - - +
989B VAL 3.3 0.6 - - - -
990B SER* 1.3 76.6 - - - +
992B ASN* 1.3 60.2 + - - +
994B GLY* 3.6 2.1 + - - -
1045B PRO* 4.4 7.9 - - + -
43J TYR* 3.5 40.2 - - + +
46J ARG* 2.8 29.6 + - - +
47J ARG* 4.7 3.1 - - + +
50J LEU* 4.7 7.6 - - - -
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Residues in contact with ASN 992 (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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988B LYS* 3.0 21.0 + - - +
989B VAL* 3.9 2.9 - - - +
990B SER 3.3 0.2 - - - -
991B ALA* 1.3 75.1 - - - +
993B LYS* 1.3 58.0 + - - +
1015B LEU* 4.1 3.8 - - - +
1018B TYR* 3.8 33.9 - - + +
1020B TYR* 3.0 46.1 + - - -
41J LYS 6.0 0.2 + - - -
43J TYR* 3.6 17.9 - - - +
46J ARG* 2.5 29.2 + - - +
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Residues in contact with LYS 993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989B VAL* 2.9 28.5 + - + +
990B SER* 4.3 1.1 - - - +
992B ASN* 1.3 73.7 - - - +
994B GLY* 1.3 58.5 + - - +
995B GLU* 3.7 32.9 - - + +
1018B TYR* 3.1 30.4 + - + +
32J GLY* 3.6 17.0 - - - -
46J ARG* 3.4 5.2 + - - -
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Residues in contact with GLY 994 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990B SER 2.7 13.0 + - - -
991B ALA 4.0 0.9 - - - -
992B ASN 3.2 2.6 - - - -
993B LYS* 1.3 78.2 - - - +
995B GLU* 1.3 59.3 + - - +
31J GLU* 4.0 14.2 - - - +
32J GLY* 4.9 2.7 - - - -
35J LEU* 4.4 7.4 - - - -
46J ARG* 3.5 11.9 - - - -
50J LEU* 3.1 36.5 - - - +
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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
------------------------------------------------------------
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