Contacts of the helix formed by residues 1022 - 1034 (chain B) in PDB entry 4E70
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 GLY1022 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY* 3.3 35.1 - - - -
25A ASN* 4.8 3.8 - - - -
26A SER* 3.2 2.2 + - - -
321A ILE* 5.5 0.7 - - - -
1018B HIS* 3.3 8.8 + - - -
1019B HIS 3.0 13.3 + - - -
1021B LEU* 1.3 76.7 - - - +
1023B TYR* 1.3 62.4 + - - +
1025B ASN* 3.0 25.3 + - - +
1026B SER 3.6 0.3 + - - -
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Residues in contact with TYR1023 (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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22A GLY 3.7 0.6 + - - -
23A TYR* 3.7 28.7 - - + +
26A SER* 3.1 21.3 + - - +
27A MET* 6.5 0.9 - - + -
122A SER 2.7 30.3 + - - -
123A VAL* 4.2 2.9 - - + -
127A LEU* 3.9 8.3 + - - +
128A VAL* 3.8 37.5 - - + -
131A TRP* 4.1 13.7 - + - -
325A LEU* 3.9 21.0 - - - +
1020B PHE 3.5 13.9 - - - -
1021B LEU* 3.1 10.7 + - + +
1022B GLY* 1.3 75.5 - - - +
1024B ILE* 1.3 78.0 + - + +
1025B ASN 3.2 0.2 - - - -
1026B SER* 3.1 5.4 + - - -
1027B MET* 2.9 42.4 + - + +
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Residues in contact with ILE1024 (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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131A TRP* 3.5 32.1 - - + +
321A ILE* 4.1 14.1 - - + +
324A MET* 3.6 28.3 - - + -
325A LEU* 4.1 18.4 - - + -
1021B LEU* 2.9 32.4 + - + +
1023B TYR* 1.3 95.1 - - + +
1025B ASN* 1.3 58.3 + - - +
1027B MET* 4.1 2.9 - - - +
1028B THR* 2.9 43.5 + - + +
1073B MET* 4.2 8.3 - - + -
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Residues in contact with ASN1025 (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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18A HIS* 5.4 0.6 + - - -
19A HIS* 3.5 23.3 - - + +
22A GLY* 4.9 3.4 - - - -
321A ILE* 3.8 16.6 - - - +
401A GOL 3.2 35.4 + - - -
1018B HIS* 4.4 1.2 + - - -
1022B GLY* 3.0 17.2 + - - +
1024B ILE* 1.3 78.4 - - - +
1026B SER* 1.3 62.5 + - - +
1028B THR* 3.2 5.9 + - - -
1029B LEU* 3.1 26.5 + - - +
1073B MET* 3.0 24.3 - - - +
1077B LEU* 3.8 16.8 - - + +
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Residues in contact with SER1026 (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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19A HIS 3.4 6.3 + - - -
20A PHE* 2.8 29.8 + - - +
22A GLY 3.2 3.3 + - - -
23A TYR* 3.1 30.2 + - - -
1022B GLY 3.6 0.4 + - - -
1023B TYR* 3.1 11.6 + - - -
1025B ASN* 1.3 79.7 - - - +
1027B MET* 1.3 63.4 + - - +
1029B LEU* 3.9 2.1 - - - +
1030B GLN* 3.0 27.4 + - - +
1123B VAL* 3.9 16.6 - - - +
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Residues in contact with MET1027 (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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23A TYR* 6.4 1.6 - - + -
128A VAL* 4.1 24.7 - - + +
131A TRP* 3.5 47.1 - - + +
132A ARG* 3.9 36.1 - - + +
1023B TYR* 2.9 27.9 + - + +
1024B ILE* 4.1 2.7 - - - +
1026B SER* 1.3 81.5 - - - +
1028B THR* 1.3 61.4 + - - +
1030B GLN* 3.4 22.8 + - - +
1031B CYS* 2.9 32.9 + - - -
1123B VAL* 4.8 7.0 - - + +
1128B VAL* 5.6 4.3 - - + -
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Residues in contact with THR1028 (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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131A TRP* 3.8 26.9 - - + -
324A MET* 3.9 25.6 - - + -
1024B ILE* 2.9 29.4 + - + +
1025B ASN* 3.2 10.0 + - - -
1027B MET* 1.3 72.5 - - - +
1029B LEU* 1.3 66.5 + - - +
1031B CYS* 3.3 5.0 + - - +
1032B ALA* 3.0 22.2 + - - +
1070B LEU* 4.0 16.9 - - + +
1073B MET* 3.7 16.5 - - + +
1074B LEU* 4.0 6.3 - - - +
1077B LEU* 4.1 5.0 - - - +
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Residues in contact with LEU1029 (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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16A VAL* 4.0 12.8 - - + -
19A HIS* 4.0 17.7 - - + -
20A PHE* 4.0 21.3 - - + -
1025B ASN 3.1 15.2 + - - +
1026B SER* 3.9 3.8 - - - +
1028B THR* 1.3 81.0 + - - +
1030B GLN* 1.3 63.0 + - - +
1032B ALA* 3.0 11.3 + - + +
1033B LEU* 3.0 28.2 + - + +
1074B LEU* 4.4 4.2 - - + +
1077B LEU* 5.3 2.9 - - + -
1079B TYR* 3.7 40.4 - - + +
1107B LEU* 4.2 23.6 - - + -
1119B THR* 4.3 9.6 - - + +
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Residues in contact with GLN1030 (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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131A TRP 5.2 2.2 + - - -
132A ARG* 4.2 20.2 + - - +
1026B SER 3.0 18.5 + - - +
1027B MET* 3.7 23.3 + - - +
1028B THR 3.3 0.2 - - - -
1029B LEU* 1.3 76.8 - - - +
1031B CYS* 1.3 58.3 + - - +
1033B LEU* 3.1 9.6 + - - +
1034B GLU* 2.8 50.1 + - - +
1119B THR* 4.7 6.2 - - + +
1120B PHE* 3.6 24.6 - - + +
1123B VAL* 3.2 31.0 - - + +
1124B HIS* 5.8 0.3 - - - -
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Residues in contact with CYS1031 (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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131A TRP* 4.2 15.3 - - - -
134A MET* 3.6 37.9 - - - -
135A SER* 3.6 19.1 - - - +
138A LEU* 5.6 0.2 - - + -
1027B MET 2.9 21.6 + - - -
1028B THR* 3.5 10.1 - - - +
1030B GLN* 1.3 75.4 - - - +
1032B ALA* 1.3 64.5 + - - +
1034B GLU* 3.1 5.4 + - - +
1035B LEU* 2.9 33.2 + - + +
1070B LEU* 4.4 16.4 - - + -
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Residues in contact with ALA1032 (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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1028B THR 3.0 13.1 + - - +
1029B LEU* 3.0 14.8 + - + +
1031B CYS* 1.3 76.6 - - - +
1033B LEU* 1.3 63.5 + - + +
1036B ASP* 3.2 1.9 + - - -
1037B ILE* 3.1 47.6 + - + +
1038B ALA 4.7 0.7 + - - -
1070B LEU* 5.1 0.4 - - - +
1074B LEU* 3.7 30.0 - - + +
1080B PHE* 5.0 4.9 - - + -
1107B LEU* 5.2 3.8 - - + -
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Residues in contact with LEU1033 (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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1029B LEU* 3.0 15.7 + - + +
1030B GLN* 3.5 6.1 - - - +
1032B ALA* 1.3 79.4 - - - +
1034B GLU* 1.3 64.9 + - - +
1036B ASP* 3.0 14.4 + - - +
1038B ALA* 6.3 0.4 - - + -
1107B LEU* 3.9 37.0 - - + +
1116B ARG* 3.0 56.2 + - + +
1119B THR* 3.5 41.3 - - + +
1120B PHE* 3.5 18.4 - - + -
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Residues in contact with GLU1034 (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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131A TRP 5.2 2.4 - - - +
132A ARG* 4.7 11.7 - - - +
135A SER* 2.7 42.1 + - - +
139A ARG* 4.0 12.3 + - - +
1030B GLN* 2.8 44.0 + - - +
1031B CYS* 3.8 9.9 + - - -
1033B LEU* 1.3 74.3 - - - +
1035B LEU* 1.3 62.0 + - - +
1036B ASP* 3.5 4.5 + - - +
1116B ARG* 5.5 0.4 - - - +
1120B PHE* 4.0 17.6 - - + -
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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
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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