Contacts of the helix formed by residues 1040 - 1057 (chain B) in PDB entry 5JPM
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 GLU1040 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038B PRO* 3.1 12.2 + - + +
1039B PRO* 1.3 84.7 - - + +
1041B THR* 1.3 63.5 + - - +
1042B LYS 3.3 0.7 - - - -
1043B ASP* 3.2 19.3 + - + +
1044B HIS* 3.1 37.2 + - + +
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Residues in contact with THR1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991B SER* 3.2 34.5 - - - +
995B LEU* 4.6 14.8 - - + +
1034B TRP* 3.9 23.2 + - - -
1037B LEU* 4.0 16.0 - - + +
1038B PRO* 2.8 26.0 + - + +
1039B PRO* 4.3 0.3 - - - +
1040B GLU* 1.3 78.9 - - + +
1042B LYS* 1.3 59.4 + - - +
1044B HIS* 3.0 14.3 + - + +
1045B ALA* 2.8 29.3 + - - +
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Residues in contact with LYS1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034B TRP* 3.5 51.8 - - + +
1039B PRO* 4.0 16.2 - - + +
1040B GLU 3.3 0.8 - - - -
1041B THR* 1.3 77.8 + - - +
1043B ASP* 1.3 64.1 + - - +
1045B ALA* 3.4 4.5 + - - +
1046B VAL* 3.2 30.8 + - + +
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Residues in contact with ASP1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039B PRO 4.5 2.6 + - - +
1040B GLU* 3.2 21.7 + - + +
1041B THR 3.2 0.4 - - - -
1042B LYS* 1.3 78.5 - - - +
1044B HIS* 1.3 65.7 + - + +
1046B VAL* 3.3 9.9 - - + +
1047B ASP* 2.9 36.0 + - - +
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Residues in contact with HIS1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B LEU 3.9 18.6 - - - +
996B SER 4.4 5.8 - - - +
997B PRO* 4.0 40.1 + - + +
1040B GLU* 3.1 28.1 + - + +
1041B THR* 3.0 17.6 + - + +
1043B ASP* 1.3 80.4 - - + +
1045B ALA* 1.3 62.7 + - - +
1047B ASP* 3.4 9.2 + - - +
1048B LEU* 3.1 29.8 + - - +
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Residues in contact with ALA1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B LEU* 3.9 25.1 - - + +
1021B THR* 4.0 13.2 - - + -
1025B SER* 4.2 11.4 - - - +
1034B TRP* 4.7 3.4 - - + -
1041B THR 2.8 14.9 + - - +
1042B LYS* 3.7 8.7 - - - +
1043B ASP 3.3 0.4 - - - -
1044B HIS* 1.3 77.0 - - - +
1046B VAL* 1.3 64.9 + - + +
1048B LEU* 3.1 5.2 + - - +
1049B ILE* 3.1 30.5 + - + +
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Residues in contact with VAL1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042B LYS* 3.2 15.2 + - + +
1043B ASP* 3.3 20.2 - - - +
1045B ALA* 1.3 78.1 - - + +
1047B ASP* 1.3 66.1 + - - +
1049B ILE* 4.1 7.4 - - - +
1050B GLN* 3.1 30.7 + - - +
1092B GLN* 4.3 26.9 - - + +
1093B VAL* 5.5 0.3 - - - +
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Residues in contact with ASP1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B ASP* 2.9 29.0 + - - +
1044B HIS* 3.7 9.9 + - - +
1045B ALA 3.2 0.2 - - - -
1046B VAL* 1.3 83.7 - - - +
1048B LEU* 1.3 57.7 + - + +
1050B GLN* 3.9 7.9 - - - +
1051B LYS* 3.0 29.9 + - - +
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Residues in contact with LEU1048 (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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994B ALA 3.9 11.0 - - - +
995B LEU* 4.8 2.2 - - - -
996B SER 3.7 18.8 - - - +
997B PRO 3.9 18.4 - - - +
998B GLY* 4.0 15.7 - - - +
999B GLY* 3.7 13.7 - - - -
1017B TYR* 3.6 31.4 - - + +
1021B THR* 4.0 22.7 - - + +
1044B HIS 3.1 22.6 + - - +
1045B ALA* 3.1 6.5 + - - +
1047B ASP* 1.3 75.5 - - + +
1049B ILE* 1.3 59.5 + - - +
1051B LYS* 3.2 12.1 + - + +
1052B GLY 2.9 23.7 + - - -
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Residues in contact with ILE1049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017B TYR 4.1 1.6 - - - +
1018B LEU* 3.2 20.6 - - + +
1021B THR* 3.7 20.4 - - + -
1022B LEU* 3.7 21.5 - - + -
1025B SER* 4.9 8.7 - - - +
1045B ALA* 3.1 22.3 + - + +
1046B VAL* 4.1 4.5 - - - +
1048B LEU* 1.3 74.9 - - - +
1050B GLN* 1.3 58.7 + - - +
1052B GLY 3.2 0.2 + - - -
1053B TYR* 2.9 27.2 + - - +
1089B ALA* 3.6 23.3 - - + +
1092B GLN* 3.4 28.0 - - + +
1093B VAL* 3.6 19.5 - - + -
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Residues in contact with GLN1050 (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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186A VAL 5.0 2.7 - - - +
187A ARG* 3.3 58.2 + - + +
188A LYS 4.7 0.6 + - - +
189A LYS* 4.3 19.8 + - - +
1046B VAL 3.1 20.0 + - - +
1047B ASP* 4.1 7.9 - - - +
1049B ILE* 1.3 76.7 - - - +
1051B LYS* 1.3 58.2 + - - +
1053B TYR* 4.0 2.1 - - + +
1054B MET* 3.0 31.2 + - + +
1092B GLN 5.3 2.4 + - - +
1093B VAL* 3.6 40.6 + - + +
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Residues in contact with LYS1051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 5.4 14.4 - - + -
1017B TYR* 4.0 41.0 + - + -
1047B ASP 3.0 19.9 + - - +
1048B LEU* 3.5 14.2 - - + +
1049B ILE 3.2 0.2 - - - -
1050B GLN* 1.3 76.9 - - - +
1052B GLY* 1.3 60.8 + - - +
1054B MET* 3.5 15.1 + - + +
1055B ARG* 3.1 25.9 + - + +
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Residues in contact with GLY1052 (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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1014B THR* 3.3 15.0 - - - +
1017B TYR* 3.9 22.4 - - - +
1018B LEU* 3.9 10.3 - - - -
1048B LEU 2.9 12.5 + - - -
1049B ILE 3.7 2.7 - - - -
1051B LYS* 1.3 74.4 - - - +
1053B TYR* 1.3 58.6 + - - +
1055B ARG 3.2 0.5 + - - -
1056B ILE* 2.9 33.4 + - - +
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Residues in contact with TYR1053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 3.2 30.7 + - - +
186A VAL* 3.4 28.9 - - - -
187A ARG* 5.1 0.4 - - - -
1018B LEU* 3.8 3.8 - - + +
1049B ILE 2.9 16.5 + - - +
1050B GLN* 4.0 5.6 - - + +
1052B GLY* 1.3 75.4 - - - +
1054B MET* 1.3 62.7 + - - +
1056B ILE* 3.8 6.1 - - - -
1057B GLN* 3.1 62.5 + - + +
1086B LEU* 4.2 25.1 - - + -
1090B GLN* 5.9 2.0 - - + -
1093B VAL* 3.8 37.7 - - + -
1094B GLY 5.1 1.3 - - - -
1095B GLY* 3.6 26.2 - - - -
1096B SER 4.3 2.8 + - - -
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Residues in contact with MET1054 (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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186A VAL* 3.9 32.9 - - + +
187A ARG* 4.2 22.4 - - + +
202A PHE* 3.8 36.3 - - + -
203A VAL* 3.4 28.7 - - + +
205A PRO* 4.1 14.3 - - + +
213A TRP* 5.3 0.9 - - + -
1050B GLN* 3.0 20.2 + - + +
1051B LYS* 3.9 12.8 - - + +
1052B GLY 3.3 0.2 - - - -
1053B TYR* 1.3 77.9 - - - +
1055B ARG* 1.3 59.3 + - - +
1057B GLN* 4.0 3.5 + - - +
1058B GLN* 3.1 28.5 + - - +
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Residues in contact with ARG1055 (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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205A PRO* 4.3 16.7 - - + +
206A ASP* 3.6 18.6 + - - +
207A ILE* 3.3 34.6 - - + +
1008B ARG 2.6 29.9 + - - -
1009B GLY* 2.8 27.3 + - - -
1010B CYS 3.4 5.1 + - - -
1014B THR* 3.0 32.5 + - + +
1017B TYR* 4.4 16.6 - - - -
1051B LYS* 3.1 19.3 + - + +
1052B GLY* 3.2 0.4 + - - -
1054B MET* 1.3 76.7 - - - +
1056B ILE* 1.3 64.9 + - - +
1057B GLN 3.2 0.4 - - - -
1058B GLN* 3.2 20.1 + - - +
1059B PHE* 3.6 8.9 - - + -
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Residues in contact with ILE1056 (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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1011B GLY 3.4 28.3 - - - +
1014B THR* 3.6 14.5 - - + +
1015B MET* 4.0 17.0 - - + -
1018B LEU* 4.5 5.6 - - + -
1052B GLY 2.9 21.7 + - - +
1053B TYR* 3.4 14.4 - - - +
1055B ARG* 1.3 77.1 - - - +
1057B GLN* 1.3 65.9 + - + +
1059B PHE* 3.1 28.0 + - + +
1066B TYR* 3.6 11.3 - - + -
1078B LEU* 5.3 3.4 - - + -
1082B VAL* 4.1 23.1 - - + -
1086B LEU* 4.0 20.4 - - + -
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Residues in contact with GLN1057 (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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180A ASN* 4.6 4.0 + - - -
184A LEU* 3.5 36.1 - - + +
185A ARG 4.6 3.6 - - - +
186A VAL* 4.9 7.6 - - + -
1053B TYR* 3.1 60.0 + - + +
1054B MET* 4.4 4.7 - - - +
1055B ARG 3.2 1.2 - - - -
1056B ILE* 1.3 78.4 - - + +
1058B GLN* 1.3 62.9 + - - +
1059B PHE 3.1 0.2 - - - -
1060B ARG* 3.3 27.3 + - - +
1066B TYR* 2.6 30.3 + - - -
1086B LEU* 4.5 5.1 - - - +
1099B LYS* 5.2 6.3 - - - +
1100B LEU* 6.3 1.0 - - - +
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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
------------------------------------------------------------
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