Contacts of the helix formed by residues 1060 - 1076 (chain A) in PDB entry 4E4N
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991A MET 6.0 0.2 - - - +
995A GLY* 4.0 30.5 - - - +
998A GLN* 5.8 2.5 - - - -
999A TYR 4.5 7.4 - - - +
1000A VAL* 3.8 8.6 - - + +
1028A ILE* 4.2 18.6 - - + +
1033A GLU 4.5 1.6 + - - +
1059A TYR* 1.3 73.6 - - - +
1061A ALA* 1.3 62.2 + - - +
1063A ASP* 3.0 20.7 + - + +
1064A VAL* 3.2 12.2 + - + +
1142A PHE* 4.7 19.3 - - + -
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Residues in contact with ALA1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A TYR* 3.1 5.5 - - + +
1060A ILE* 1.3 80.2 - - - +
1062A SER* 1.3 56.4 + - - +
1064A VAL* 3.2 14.1 + - - +
1065A TRP 3.1 18.7 + - - -
1136A PRO* 3.5 44.4 - - + +
1139A ARG* 3.1 19.2 + - + +
1140A THR 5.8 0.4 - - - +
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Residues in contact with SER1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A ALA* 4.3 4.8 + - - +
1051A GLU* 2.5 32.1 + - - +
1052A CYS* 3.5 22.4 - - - -
1058A PHE* 4.3 5.8 - - - -
1059A TYR* 3.0 30.8 + - - +
1061A ALA* 1.3 76.0 - - - +
1063A ASP* 1.3 59.0 + - - +
1065A TRP* 3.4 4.5 + - - +
1066A SER* 3.1 28.5 + - - -
1139A ARG* 3.8 2.2 - - - +
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Residues in contact with ASP1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991A MET* 3.4 26.9 - - + +
994A LEU* 4.9 0.5 - - - +
999A TYR 4.4 2.8 - - - +
1000A VAL* 3.5 11.6 - - - +
1001A HIS* 2.8 24.7 + - - +
1002A ARG* 3.1 26.5 + - - +
1003A ASP 4.8 0.5 + - - -
1004A LEU* 4.0 4.2 - - - +
1058A PHE* 6.0 0.5 - - - -
1059A TYR 3.5 5.5 + - - -
1060A ILE* 3.0 13.4 + - + +
1062A SER* 1.3 77.3 - - - +
1064A VAL* 1.3 57.5 + - - +
1066A SER* 3.3 9.9 + - - -
1067A PHE* 2.8 28.9 + - - +
1142A PHE* 3.7 8.8 - - + -
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Residues in contact with VAL1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A ILE* 3.2 13.6 + - + +
1061A ALA* 3.2 13.6 + - - +
1063A ASP* 1.3 75.3 - - - +
1065A TRP* 1.3 65.0 + - - +
1067A PHE* 3.1 5.2 + - - +
1068A GLY 3.0 18.4 + - - -
1131A CYS* 3.5 28.9 - - + +
1139A ARG* 4.4 4.3 - - + -
1140A THR* 3.4 36.1 - - + +
1141A SER* 4.5 1.8 - - - -
1142A PHE* 3.7 39.5 - - + +
1145A LEU* 4.3 3.4 - - + -
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Residues in contact with TRP1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A PHE 5.5 0.8 + - - -
1047A TRP 3.4 19.4 + - - -
1048A TYR 3.4 9.9 + - - -
1049A ALA* 3.6 23.3 - - + -
1050A PRO* 3.5 26.0 - - + -
1061A ALA 3.1 11.1 + - - +
1062A SER 3.5 8.5 - - - +
1064A VAL* 1.3 76.9 - - - +
1066A SER* 1.3 61.4 + - - +
1068A GLY 3.2 9.9 + - - -
1069A VAL* 3.3 14.7 + - + +
1088A PHE* 5.8 3.5 - + - -
1108A LEU* 3.8 29.2 - - + -
1113A ARG* 3.8 22.4 - - - -
1131A CYS 3.3 12.5 + - - +
1132A TRP* 3.2 54.9 + + + -
1133A GLU 3.6 7.0 - - - -
1139A ARG* 3.5 17.9 - - - +
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Residues in contact with SER1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A ARG* 5.5 2.8 - - - -
1004A LEU* 3.8 29.1 + - - +
1047A TRP* 2.9 26.6 + - - +
1048A TYR* 4.6 9.5 - - - -
1049A ALA 5.2 0.2 + - - -
1062A SER 3.1 15.6 + - - -
1063A ASP* 3.3 13.3 + - - -
1065A TRP* 1.3 72.1 - - - +
1067A PHE* 1.3 59.6 + - - +
1069A VAL* 3.3 6.3 + - - +
1070A THR* 2.9 31.6 + - - -
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Residues in contact with PHE1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984A ALA* 3.8 17.9 - - + -
987A ILE* 3.7 35.0 - - + -
988A CYS* 3.4 28.5 - - - -
1004A LEU* 3.6 14.1 - - + +
1063A ASP 2.8 14.0 + - - +
1064A VAL 3.1 7.2 + - - +
1066A SER* 1.3 75.1 - - - +
1068A GLY* 1.3 57.0 + - - +
1070A THR* 3.1 5.0 + - - -
1071A LEU* 2.7 50.7 + - + +
1074A LEU* 6.5 0.2 - - + -
1131A CYS* 4.1 4.5 - - - -
1142A PHE* 3.7 13.0 - + + -
1145A LEU* 3.8 26.2 - - + -
1149A PHE* 3.9 22.7 - + - -
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Residues in contact with GLY1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064A VAL 3.0 11.1 + - - -
1065A TRP 3.2 5.5 + - - -
1067A PHE* 1.3 78.4 - - - +
1069A VAL* 1.3 56.2 + - - +
1071A LEU* 3.4 7.6 + - - +
1072A HIS 3.0 20.6 + - - -
1128A MET* 3.5 6.9 - - - +
1131A CYS* 3.8 19.3 - - - -
1132A TRP* 3.4 23.8 - - - -
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Residues in contact with VAL1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A PHE 3.9 13.9 - - - +
1047A TRP* 3.6 21.1 - - + +
1065A TRP* 3.3 28.9 + - + +
1066A SER 3.3 6.0 + - - +
1067A PHE 3.2 0.4 - - - -
1068A GLY* 1.3 73.4 - - - +
1070A THR* 1.3 64.6 + - - +
1072A HIS* 3.2 5.7 + - - +
1073A GLU* 3.1 22.0 + - - +
1084A PRO* 3.4 35.2 - - + -
1088A PHE* 5.6 2.5 - - + -
1114A LEU* 4.0 9.9 - - + -
1132A TRP* 3.6 19.7 - - + +
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Residues in contact with THR1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964A LEU* 5.3 2.5 - - + -
987A ILE* 4.5 14.6 - - + -
1004A LEU* 3.2 26.5 + - + +
1005A ALA* 3.3 9.6 - - - +
1006A ALA* 3.8 25.3 - - + +
1009A VAL* 4.5 12.3 - - + -
1047A TRP* 4.2 0.3 - - - -
1066A SER 2.9 14.7 + - - -
1067A PHE* 3.5 13.0 - - + -
1069A VAL* 1.3 75.8 - - - +
1071A LEU* 1.3 58.1 + - - +
1073A GLU* 3.2 12.2 + - - +
1074A LEU* 3.0 26.3 + - + +
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Residues in contact with LEU1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980A GLN 5.4 0.4 - - - +
981A LEU* 5.3 2.9 - - + -
984A ALA* 3.9 26.5 - - + -
987A ILE* 6.6 0.4 - - - -
1067A PHE* 2.7 34.5 + - + +
1068A GLY* 3.5 7.2 - - - +
1070A THR* 1.3 70.5 - - - +
1072A HIS* 1.3 63.7 + - - +
1074A LEU* 3.3 12.4 + - + +
1075A LEU* 3.0 51.4 + - + +
1124A VAL* 4.7 6.3 - - + +
1128A MET* 4.0 32.5 - - + +
1131A CYS* 5.7 0.2 - - - -
1145A LEU* 5.8 0.2 - - + -
1149A PHE* 3.8 28.7 - - + -
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Residues in contact with HIS1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A GLY 3.0 13.1 + - - +
1069A VAL* 3.2 13.0 + - + +
1071A LEU* 1.3 76.5 - - - +
1073A GLU* 1.3 62.0 + - - +
1075A LEU* 3.4 1.9 + - - +
1076A THR* 3.1 50.9 + - + +
1082A SER 4.1 5.3 + - - -
1084A PRO* 5.5 4.0 - - - +
1087A LEU* 3.6 28.5 - - + +
1114A LEU* 3.9 27.4 - - + +
1115A PRO* 2.7 30.6 + - + +
1117A PRO* 3.7 16.5 - - + +
1128A MET* 3.8 22.2 - - - +
1132A TRP* 4.4 0.4 - + + -
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Residues in contact with GLU1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A LYS* 4.6 13.3 + - - +
1005A ALA* 5.1 0.2 - - - +
1006A ALA* 3.0 40.8 + - + +
1007A ARG 4.8 1.2 + - - -
1047A TRP* 2.9 40.6 + - - -
1069A VAL 3.1 13.6 + - - +
1070A THR* 3.2 12.0 + - - +
1072A HIS* 1.3 75.0 - - - +
1074A LEU* 1.3 65.5 + - - +
1076A THR* 3.1 8.8 + - - -
1077A TYR 3.1 3.8 + - - -
1078A CYS* 2.8 37.3 + - - +
1082A SER 6.2 0.2 - - - -
1083A SER* 5.6 0.4 - - - -
1084A PRO* 3.8 21.7 - - + +
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Residues in contact with LEU1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964A LEU* 4.4 11.7 - - + -
968A LEU* 3.6 27.1 - - + +
980A GLN* 2.9 57.7 + - + +
983A TYR* 3.9 32.8 - - + -
984A ALA* 4.1 14.6 - - + +
987A ILE* 4.8 9.4 - - + -
1006A ALA* 5.2 0.4 - - - +
1067A PHE* 6.5 0.2 - - + -
1070A THR* 3.0 13.6 + - + +
1071A LEU* 3.6 16.8 - - + +
1073A GLU* 1.3 75.3 - - - +
1075A LEU* 1.3 58.1 + - + +
1077A TYR* 3.1 15.4 + - - -
1078A CYS* 5.0 0.2 - - - -
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Residues in contact with LEU1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977A LEU* 4.1 18.8 - - + -
980A GLN* 3.5 32.5 + - + +
981A LEU* 5.2 1.6 - - + -
1071A LEU* 3.0 32.4 + - + +
1072A HIS 3.7 4.7 - - - +
1073A GLU 3.2 0.2 - - - -
1074A LEU* 1.3 77.6 - - + +
1076A THR* 1.3 57.4 + - - +
1077A TYR* 3.3 9.9 + - - -
1117A PRO* 3.8 16.7 - - + +
1118A PRO* 4.5 7.6 - - - +
1120A CYS* 3.7 22.9 - - + -
1124A VAL* 4.0 11.2 - - + -
1128A MET* 3.2 34.8 - - + -
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Residues in contact with THR1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A LYS* 5.0 2.1 + - - -
1072A HIS* 3.1 32.1 + - + +
1073A GLU* 3.1 14.9 + - - -
1075A LEU* 1.3 73.9 - - - +
1077A TYR* 1.3 70.3 + - - +
1078A CYS* 3.7 4.2 + - - -
1079A ASP* 3.2 21.4 + - - +
1082A SER* 4.1 27.8 + - - -
1083A SER* 5.7 0.5 - - - -
1117A PRO* 3.6 24.0 - - + -
1118A PRO* 4.7 8.3 - - + -
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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