Contacts of the helix formed by residues 1019 - 1033 (chain B) in PDB entry 2EYQ
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 ASP1019 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B ASP* 3.5 31.6 + - - +
1017B ILE* 3.4 4.1 - - + +
1018B PRO* 1.3 76.7 - - - +
1020B VAL* 1.3 67.0 + - - +
1021B ASN* 3.8 12.6 + - - +
1022B THR* 2.8 46.8 + - - +
1023B ARG* 3.1 13.4 + - - +
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Residues in contact with VAL1020 (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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493B TYR* 3.9 17.5 - - - +
495B GLY* 5.9 0.2 - - - -
496B MET* 3.7 31.1 - - + +
1018B PRO 3.0 11.2 + - - +
1019B ASP* 1.3 71.6 + - - +
1021B ASN* 1.3 65.8 + - - +
1022B THR 3.1 0.3 + - - -
1023B ARG* 3.1 27.8 + - - +
1024B LEU* 2.9 22.2 + - - +
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Residues in contact with ASN1021 (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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474B LEU 3.7 6.6 - - - +
475B ALA* 5.0 0.7 - - - -
476B GLU* 3.0 19.1 + - - +
477B LEU* 2.4 53.7 + - - +
478B HIS* 5.4 2.8 - - - -
493B TYR* 4.7 7.8 + - - -
1019B ASP* 3.2 14.2 + - - +
1020B VAL* 1.3 81.0 - - - +
1022B THR* 1.3 60.2 + - - +
1024B LEU* 3.6 7.6 - - - +
1025B SER* 3.2 19.8 + - - -
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Residues in contact with THR1022 (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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154B ASP* 5.0 1.9 + - - -
155B GLN* 4.7 10.4 + - - -
1017B ILE* 4.1 13.5 - - + -
1019B ASP* 2.8 29.3 + - - +
1021B ASN* 1.3 72.9 - - - +
1023B ARG* 1.3 69.7 + - - +
1024B LEU 3.1 1.6 - - - -
1025B SER* 2.9 9.5 + - - -
1026B PHE* 2.8 46.4 + - + -
1049B ARG* 4.3 12.6 + - - +
1050B PHE* 4.5 6.3 - - + -
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Residues in contact with ARG1023 (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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496B MET* 4.3 3.2 - - + +
507B GLU* 3.3 30.5 + - - -
1012B LEU* 3.2 48.3 + - + +
1013B PRO 3.9 5.3 + - - -
1014B ASP* 4.2 20.9 + - - +
1017B ILE* 2.8 44.2 + - + +
1018B PRO 3.1 17.2 + - - -
1019B ASP 3.1 2.6 + - - +
1020B VAL* 3.3 34.4 - - - +
1022B THR* 1.3 80.4 - - - +
1024B LEU* 1.3 64.4 + - - +
1026B PHE* 3.0 3.6 + - - +
1027B TYR* 2.8 34.4 + - + -
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Residues in contact with LEU1024 (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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474B LEU* 4.1 23.8 - - + +
477B LEU* 4.0 30.3 - - + -
493B TYR* 4.2 15.9 - - + +
496B MET* 3.5 30.9 - - + +
509B LEU* 3.7 17.3 - - + -
526B LEU* 4.1 21.3 - - + -
1020B VAL 2.9 15.6 + - - +
1021B ASN* 3.6 8.3 - - - +
1023B ARG* 1.3 76.6 - - - +
1025B SER* 1.3 64.4 + - - +
1027B TYR* 2.9 18.9 + - + +
1028B LYS* 2.9 13.2 + - - +
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Residues in contact with SER1025 (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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473B ASN* 2.8 34.6 + - - +
474B LEU 3.7 6.7 - - - -
475B ALA* 4.3 10.3 - - - +
1021B ASN 3.2 11.7 + - - -
1022B THR* 2.9 13.6 + - - -
1024B LEU* 1.3 80.9 - - - +
1026B PHE* 1.3 60.2 + - - +
1028B LYS* 3.6 3.1 + - - +
1029B ARG* 3.1 33.1 + - - +
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Residues in contact with PHE1026 (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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1012B LEU* 3.7 16.2 - - + -
1017B ILE* 4.6 2.9 - - + -
1022B THR* 2.8 35.3 + - + +
1023B ARG* 3.6 7.2 - - - +
1025B SER* 1.3 71.9 - - - +
1027B TYR* 1.3 69.4 + - - +
1029B ARG* 3.7 22.5 - - - +
1030B ILE* 3.0 26.5 + - + +
1042B ILE* 3.8 19.3 - - + -
1045B GLU* 3.4 17.7 - - + -
1046B LEU* 3.2 40.8 - - + -
1049B ARG* 3.3 37.0 - - - -
1050B PHE* 4.2 7.4 - + - -
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Residues in contact with TYR1027 (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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496B MET* 4.1 5.2 - - + -
507B GLU* 3.3 34.5 + - + -
523B VAL* 3.2 54.7 - - + +
526B LEU* 4.3 9.4 - - + -
1011B LEU* 3.3 8.0 - - - +
1012B LEU* 2.8 43.0 + - + -
1023B ARG* 2.8 31.7 + - + -
1024B LEU* 2.9 12.1 + - + +
1026B PHE* 1.3 71.9 - - - +
1028B LYS* 1.3 69.6 + - - +
1030B ILE* 2.8 18.6 + - - +
1031B ALA* 2.9 14.9 + - - +
1060B LEU* 3.7 20.0 - - + -
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Residues in contact with LYS1028 (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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472B ARG* 3.1 36.8 + - - +
473B ASN* 4.8 4.7 - - - +
474B LEU* 3.6 33.0 - - + -
526B LEU* 3.6 28.6 - - + +
527B HIS* 4.8 2.2 + - - +
529B ILE 3.3 27.1 + - - -
530B SER* 4.8 3.2 + - - +
1024B LEU 2.9 12.2 + - - +
1025B SER* 3.8 6.1 - - - +
1027B TYR* 1.3 78.2 - - - +
1029B ARG* 1.3 64.9 + - - +
1031B ALA* 3.2 1.0 + - - +
1032B SER* 2.8 45.0 + - - +
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Residues in contact with ARG1029 (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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473B ASN* 3.4 42.0 - - - +
1025B SER* 3.1 21.1 + - - +
1026B PHE* 3.7 22.5 - - - +
1028B LYS* 1.3 82.1 - - - +
1030B ILE* 1.3 64.6 + - - +
1032B SER* 3.1 11.5 + - - -
1033B ALA* 3.1 13.0 + - - +
1041B GLU* 5.6 4.9 - - - +
1042B ILE* 3.8 36.2 - - + +
1045B GLU* 3.3 39.8 + - - -
1049B ARG* 5.0 0.4 - - - +
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Residues in contact with ILE1030 (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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1012B LEU* 4.9 2.7 - - + -
1026B PHE 3.0 20.6 + - - +
1027B TYR* 2.8 11.5 + - + +
1029B ARG* 1.3 71.5 - - - +
1031B ALA* 1.3 66.6 + - - +
1033B ALA* 3.2 17.3 + - - +
1039B LEU* 4.2 8.0 - - + +
1042B ILE* 3.7 25.6 - - + -
1046B LEU* 4.6 9.6 - - + -
1060B LEU* 3.5 32.8 - - + +
1061B LEU* 3.3 28.5 - - + -
1064B ALA* 3.7 30.2 - - + +
1068B GLN* 5.6 0.2 + - - -
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Residues in contact with ALA1031 (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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523B VAL 4.2 7.2 - - - +
524B SER* 4.4 11.0 - - - +
526B LEU* 4.0 12.8 - - + +
527B HIS* 3.7 32.9 - - + +
1027B TYR 2.9 11.9 + - - +
1028B LYS 3.5 8.3 - - - +
1030B ILE* 1.3 82.2 - - - +
1032B SER* 1.3 57.1 + - - +
1033B ALA 3.1 10.4 + - - +
1064B ALA* 5.9 1.1 - - - -
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Residues in contact with SER1032 (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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472B ARG* 6.0 4.0 - - - -
473B ASN* 6.1 0.2 - - - -
527B HIS* 3.6 20.3 + - - +
1028B LYS* 2.8 47.8 + - - +
1029B ARG* 3.6 5.2 - - - -
1031B ALA* 1.3 68.8 - - - +
1033B ALA* 1.3 65.5 + - - +
1034B LYS* 3.8 13.4 + - - +
1038B GLU* 5.1 0.2 - - - +
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Residues in contact with ALA1033 (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 ARG 3.1 9.0 + - - +
1030B ILE* 3.3 16.6 - - - +
1031B ALA 3.1 8.4 + - - +
1032B SER* 1.3 82.0 - - - +
1034B LYS* 1.3 63.1 + - - +
1038B GLU* 4.0 19.7 - - + -
1039B LEU* 4.1 25.6 - - + +
1042B ILE* 4.8 3.6 - - + -
1068B GLN* 3.4 10.2 + - - +
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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
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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