Contacts of the helix formed by residues 1060 - 1076 (chain B) in PDB entry 4E5W
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 ILE1060 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B GLY* 3.6 34.5 - - - +
998B GLN* 4.7 7.9 - - - +
999B TYR 4.2 8.3 - - - +
1000B VAL* 3.7 8.0 - - + +
1028B ILE* 3.8 26.0 - - + -
1033B GLU 4.4 3.4 + - - -
1059B TYR* 1.3 72.6 - - - +
1061B ALA* 1.4 58.0 + - - +
1063B ASP* 2.9 25.1 + - + +
1064B VAL* 3.2 13.0 + - + +
1142B PHE* 4.9 17.0 - - + -
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Residues in contact with ALA1061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B TYR* 3.2 5.4 - - + +
1060B ILE* 1.4 78.1 - - - +
1062B SER* 1.3 59.1 + - - +
1064B VAL* 3.3 14.7 + - - +
1065B TRP 3.2 15.2 + - - -
1136B PRO* 3.5 43.7 - - + +
1139B ARG* 3.1 20.2 + - + +
1140B THR 5.9 0.2 - - - +
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Residues in contact with SER1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049B ALA* 4.2 4.7 + - - +
1051B GLU* 2.6 28.8 + - - -
1052B CYS* 3.6 20.3 - - - -
1058B PHE* 3.5 16.2 - - - -
1059B TYR* 3.0 31.4 + - - +
1061B ALA* 1.3 76.0 - - - +
1063B ASP* 1.3 60.5 + - - +
1065B TRP* 3.4 5.0 + - - +
1066B SER* 3.2 24.1 + - - -
1139B ARG* 3.8 3.1 - - - +
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Residues in contact with ASP1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991B MET* 3.6 26.1 - - + +
994B LEU* 5.1 0.2 - - - +
999B TYR 4.4 2.8 - - - +
1000B VAL* 3.4 10.9 - - - +
1001B HIS* 2.7 26.9 + - - +
1002B ARG* 3.1 23.4 + - - -
1003B ASP 4.7 0.7 + - - -
1004B LEU* 4.0 5.9 - - - +
1058B PHE* 3.1 12.8 - - - -
1059B TYR 3.5 1.7 + - - -
1060B ILE* 2.9 14.4 + - + +
1062B SER* 1.3 77.0 - - - +
1064B VAL* 1.4 57.7 + - - +
1066B SER* 3.3 8.1 + - - -
1067B PHE* 2.9 28.1 + - - +
1142B PHE* 3.8 8.1 - - + -
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Residues in contact with VAL1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060B ILE* 3.2 14.8 + - + +
1061B ALA* 3.3 14.6 + - - +
1063B ASP* 1.4 73.5 - - - +
1065B TRP* 1.4 63.2 - - - +
1067B PHE* 3.1 5.1 + - - +
1068B GLY 3.0 17.3 + - - -
1131B CYS* 3.4 19.3 - - - +
1139B ARG* 4.7 3.1 - - + -
1140B THR* 3.2 44.2 - - + +
1141B SER* 4.6 0.9 - - - -
1142B PHE* 3.6 38.4 - - + +
1145B LEU* 4.2 6.3 - - + -
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Residues in contact with TRP1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B PHE 5.3 1.2 + - - -
1047B TRP 3.4 20.8 + - - -
1048B TYR 3.4 10.3 + - - -
1049B ALA* 3.5 23.1 - - + -
1050B PRO* 3.5 24.7 - - + -
1061B ALA 3.2 10.6 + - - +
1062B SER 3.5 9.0 - - - +
1063B ASP 3.3 0.2 - - - -
1064B VAL* 1.4 73.3 - - - +
1066B SER* 1.3 61.7 + - - +
1068B GLY 3.1 11.1 + - - -
1069B VAL* 3.3 15.1 + - + +
1088B PHE* 5.6 5.4 - + - -
1108B LEU* 3.9 28.7 - - + -
1113B ARG* 3.7 26.5 - - - -
1131B CYS 3.3 12.2 + - - +
1132B TRP* 3.2 60.4 + + + -
1133B GLU 3.8 4.9 - - - -
1139B ARG* 3.7 18.8 - - - +
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Residues in contact with SER1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ARG 5.6 0.3 - - - -
1004B LEU* 3.7 29.6 + - - +
1047B TRP* 2.8 26.8 + - - +
1048B TYR* 4.3 11.4 - - - -
1058B PHE* 4.5 5.0 - - - -
1062B SER 3.2 11.3 + - - -
1063B ASP* 3.3 11.9 + - - -
1065B TRP* 1.3 78.2 - - - +
1067B PHE* 1.3 56.8 + - - +
1069B VAL* 3.3 6.2 + - - +
1070B THR* 2.9 31.7 + - - -
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Residues in contact with PHE1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984B ALA* 3.7 24.2 - - + -
987B ILE* 3.7 31.9 - - + -
988B CYS* 3.4 28.3 - - - -
1004B LEU* 3.7 10.0 - - + +
1063B ASP 2.9 9.9 + - - +
1064B VAL 3.1 7.6 + - - +
1066B SER* 1.3 73.9 - - - +
1068B GLY* 1.3 57.3 + - - +
1070B THR* 3.1 4.9 + - - -
1071B LEU* 2.7 50.7 + - + +
1074B LEU* 5.9 0.2 - - + -
1131B CYS* 4.0 4.5 - - - -
1142B PHE* 3.6 22.0 - + + -
1145B LEU* 3.7 22.7 - - + -
1149B PHE* 3.8 24.7 - + - -
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Residues in contact with GLY1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064B VAL 3.0 10.7 + - - -
1065B TRP 3.1 5.7 + - - -
1067B PHE* 1.3 76.8 - - - +
1069B VAL* 1.3 56.2 + - - +
1071B LEU* 3.4 8.2 + - - +
1072B HIS 3.1 20.4 + - - -
1128B MET* 3.6 8.8 - - - +
1131B CYS* 3.8 18.2 - - - -
1132B TRP* 3.4 25.2 - - - -
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Residues in contact with VAL1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B PHE 3.8 11.9 - - - +
1047B TRP* 3.4 24.5 - - + -
1065B TRP* 3.3 28.9 + - + +
1066B SER 3.6 6.5 - - - +
1067B PHE 3.2 0.4 - - - -
1068B GLY* 1.3 72.9 - - - +
1070B THR* 1.4 63.9 + - - +
1072B HIS* 3.2 6.4 + - - +
1073B GLU* 3.0 21.9 + - - +
1084B PRO* 3.4 34.5 - - + +
1088B PHE* 5.6 2.2 - - + -
1114B LEU* 4.2 7.6 - - + -
1132B TRP* 3.7 20.0 - - + +
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Residues in contact with THR1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964B LEU* 5.6 1.3 - - + -
987B ILE* 4.4 23.8 - - + -
1004B LEU* 3.2 27.3 + - + +
1005B ALA* 3.3 9.4 - - - +
1006B ALA* 3.8 23.2 - - + +
1009B VAL* 4.6 5.2 - - + -
1047B TRP* 4.2 0.3 - - - -
1066B SER 2.9 13.8 + - - -
1067B PHE* 3.1 13.4 + - + -
1069B VAL* 1.4 75.2 - - - +
1071B LEU* 1.3 56.5 + - - +
1073B GLU* 3.2 14.0 + - - +
1074B LEU* 3.0 28.2 + - + +
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Residues in contact with LEU1071 (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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980B GLN 5.4 1.3 - - - +
981B LEU* 5.1 3.8 - - + -
984B ALA* 3.8 29.2 - - + -
1067B PHE* 2.7 32.7 + - + +
1068B GLY* 3.5 5.2 - - - +
1070B THR* 1.3 70.5 - - - +
1072B HIS* 1.3 63.6 + - - +
1074B LEU* 3.2 15.4 + - + +
1075B LEU* 3.0 46.3 + - + +
1124B VAL* 4.7 6.7 - - + +
1127B LEU 5.2 0.4 - - - -
1128B MET* 4.0 33.4 - - + +
1131B CYS* 5.8 0.2 - - - -
1145B LEU* 5.8 0.2 - - + -
1149B PHE* 3.8 27.6 - - + -
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Residues in contact with HIS1072 (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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1068B GLY 3.1 13.1 + - - +
1069B VAL* 3.2 13.2 + - - +
1071B LEU* 1.3 75.2 - - - +
1073B GLU* 1.3 61.5 + - - +
1075B LEU* 3.3 2.6 + - - +
1076B THR* 3.1 49.6 + - + +
1082B SER 4.3 4.4 + - - -
1084B PRO* 5.2 4.0 - - + +
1087B LEU* 3.6 29.0 - - + +
1114B LEU* 3.9 28.0 - - + +
1115B PRO* 2.7 29.0 + - + +
1117B PRO* 3.6 16.4 - - + +
1128B MET* 3.8 22.8 - - - +
1132B TRP* 4.6 0.2 - - + -
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Residues in contact with GLU1073 (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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965B LYS* 4.6 13.7 + - - +
1005B ALA* 5.0 0.2 - - - +
1006B ALA* 2.9 44.8 + - + +
1007B ARG* 4.8 2.4 + - - -
1047B TRP* 2.9 36.3 + - - -
1069B VAL 3.0 16.5 + - - +
1070B THR* 3.2 11.7 + - - +
1072B HIS* 1.3 73.7 - - - +
1074B LEU* 1.3 62.8 + - - +
1076B THR* 3.2 8.5 + - - -
1077B TYR 3.1 3.5 + - - -
1078B CYS* 2.8 39.2 + - - +
1083B SER* 5.8 0.4 - - - +
1084B PRO* 3.7 20.9 - - + +
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Residues in contact with LEU1074 (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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964B LEU* 4.2 12.3 - - + -
968B LEU* 3.6 26.1 - - + +
980B GLN* 3.0 47.4 + - + +
983B TYR* 3.8 29.2 - - + -
984B ALA* 4.2 9.6 - - + +
987B ILE* 4.0 25.1 - - + -
1006B ALA* 5.3 0.2 - - - +
1067B PHE* 5.9 0.7 - - + -
1070B THR* 3.0 13.4 + - + +
1071B LEU* 3.3 17.9 - - + +
1073B GLU* 1.3 75.1 - - - +
1075B LEU* 1.3 59.6 + - + +
1077B TYR* 3.0 16.3 + - - -
1078B CYS* 4.7 0.9 - - - -
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Residues in contact with LEU1075 (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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977B LEU* 3.8 29.2 - - + -
980B GLN* 3.6 26.5 + - + +
981B LEU* 5.1 2.9 - - + -
1071B LEU* 3.0 20.7 + - + +
1072B HIS 3.8 4.0 - - - +
1074B LEU* 1.3 80.7 - - + +
1076B THR* 1.4 58.0 + - - +
1077B TYR* 3.3 10.1 + - - -
1117B PRO* 3.9 16.9 - - + +
1118B PRO* 4.6 7.8 - - - +
1120B CYS* 3.7 24.7 - - + -
1124B VAL* 3.9 14.8 - - + -
1128B MET* 3.5 31.4 - - + -
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Residues in contact with THR1076 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972B LYS* 5.5 0.7 + - - -
1072B HIS* 3.1 38.6 + - + +
1073B GLU* 3.2 15.2 + - - -
1075B LEU* 1.4 74.4 - - - +
1077B TYR* 1.4 68.9 + - - +
1078B CYS* 3.8 3.1 + - - -
1079B ASP* 3.2 21.8 + - - +
1082B SER* 4.1 28.4 + - - -
1083B SER* 5.6 0.5 - - - -
1117B PRO* 3.8 17.3 - - + -
1118B PRO* 4.6 9.2 - - + -
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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
------------------------------------------------------------
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