Contacts of the helix formed by residues 1025 - 1039 (chain B) in PDB entry 4DQL
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 SER1025 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1019B ALA* 4.2 1.1 - - - +
1024B VAL* 1.3 81.3 - - - +
1026B GLU* 1.3 63.5 + - - +
1027B ALA* 2.9 17.1 + - - +
1028B ASP* 2.9 30.8 + - - -
1029B ALA* 3.1 18.9 + - - +
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Residues in contact with GLU1026 (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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1015B MET* 5.0 2.8 - - - +
1016B LYS* 6.5 0.9 - - - -
1019B ALA* 4.8 7.9 - - + +
1024B VAL 3.8 0.6 + - - -
1025B SER* 1.3 72.4 - - - +
1027B ALA* 1.3 56.7 + - - +
1029B ALA* 3.5 8.1 + - - +
1030B ARG* 3.1 27.0 + - - +
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Residues in contact with ALA1027 (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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1025B SER* 2.9 12.0 - - - +
1026B GLU* 1.3 76.3 - - - +
1028B ASP* 1.3 63.7 + - - +
1029B ALA 3.2 1.6 - - - -
1030B ARG* 3.5 6.8 + - - +
1031B LEU* 3.3 21.1 + - - +
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Residues in contact with ASP1028 (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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1018B TYR* 4.9 1.9 - - + -
1024B VAL* 3.2 34.9 - - + +
1025B SER* 2.9 19.0 + - - +
1027B ALA* 1.3 78.6 - - - +
1029B ALA* 1.3 56.7 + - - +
1031B LEU* 3.4 17.2 + - - +
1032B TRP* 3.0 27.2 + - - +
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Residues in contact with ALA1029 (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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1015B MET* 3.5 37.4 - - + +
1018B TYR* 4.2 18.4 - - + -
1019B ALA* 4.0 9.9 - - + -
1024B VAL* 4.5 0.2 - - + -
1025B SER 3.1 15.5 + - - +
1026B GLU* 3.8 6.5 - - - +
1027B ALA 3.2 0.2 - - - -
1028B ASP* 1.3 74.8 - - - +
1030B ARG* 1.3 66.0 + - - +
1032B TRP* 3.2 8.9 + - - +
1033B LEU* 3.2 20.8 + - - +
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Residues in contact with ARG1030 (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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1015B MET* 3.6 24.9 - - + -
1026B GLU 3.1 17.4 + - - +
1027B ALA* 3.8 7.4 - - - +
1028B ASP 3.4 0.2 - - - -
1029B ALA* 1.3 75.5 - - - +
1031B LEU* 1.3 60.6 + - - +
1033B LEU* 3.3 4.3 + - - +
1034B GLN* 3.1 43.8 + - + +
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Residues in contact with LEU1031 (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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1027B ALA 3.3 10.8 + - - +
1028B ASP* 3.6 20.4 - - - +
1029B ALA 3.2 0.4 - - - -
1030B ARG* 1.3 80.0 - - - +
1032B TRP* 1.3 62.4 + - - +
1034B GLN* 3.3 18.9 + - + +
1035B GLN* 3.0 55.8 + - + +
1038B GLU* 5.7 2.5 - - - +
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Residues in contact with TRP1032 (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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988B ILE* 3.9 20.2 - - + -
991B LEU* 4.1 19.5 - - + +
992B ASP* 4.7 5.1 + - - -
1014B LEU* 4.1 24.2 - - + -
1015B MET* 4.6 4.9 - - + -
1018B TYR* 3.3 65.8 - + + +
1028B ASP 3.0 17.9 + - - +
1029B ALA 3.2 11.2 + - - +
1031B LEU* 1.3 78.6 - - - +
1033B LEU* 1.3 79.7 + - + +
1035B GLN* 3.5 16.8 - - - +
1036B LEU* 3.0 51.6 + - + +
1039B LYS* 6.4 0.2 - - - -
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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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997B PHE* 6.5 0.2 - - + -
1011B GLU* 3.3 43.3 - - + +
1014B LEU* 4.7 11.7 - - + -
1015B MET* 3.7 19.1 - - + -
1029B ALA 3.2 12.8 + - - +
1030B ARG 3.7 6.7 - - - +
1031B LEU 3.3 0.4 - - - -
1032B TRP* 1.3 90.9 - - + +
1034B GLN* 1.3 64.5 + - - +
1036B LEU* 3.3 18.0 + - + -
1037B GLU* 3.1 22.0 + - - +
1042B TYR* 3.5 31.5 - - + -
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Residues in contact with GLN1034 (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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1030B ARG* 3.1 30.5 + - + +
1031B LEU* 3.5 31.8 - - + +
1033B LEU* 1.3 72.7 - - + +
1035B GLN* 1.3 67.1 + - - +
1037B GLU* 3.1 10.8 + - - +
1038B GLU* 2.9 32.8 + - - +
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Residues in contact with GLN1035 (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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1031B LEU* 3.0 46.0 + - + +
1032B TRP* 3.5 15.9 + - - +
1034B GLN* 1.3 81.8 - - - +
1036B LEU* 1.3 51.2 + - - +
1038B GLU* 2.9 21.6 + - - +
1039B LYS* 2.7 58.2 + - - +
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Residues in contact with LEU1036 (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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991B LEU* 3.9 37.7 - - + +
995B ALA 5.2 0.2 - - - +
997B PHE* 4.7 3.6 - - + -
1014B LEU* 5.3 0.7 - - + -
1032B TRP* 3.0 41.4 + - + +
1033B LEU* 3.4 27.1 - - + +
1034B GLN 3.2 0.4 - - - -
1035B GLN* 1.3 74.3 - - - +
1037B GLU* 1.3 61.1 + - - +
1039B LYS* 3.3 20.2 + - + +
1040B GLY 3.3 0.2 + - - -
1041B ARG* 2.9 60.8 + - + +
1042B TYR* 4.0 6.1 - - + -
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Residues in contact with GLU1037 (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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887B SER* 5.1 7.8 + - - -
1033B LEU 3.1 12.7 + - - +
1034B GLN* 3.3 11.6 - - - +
1035B GLN 3.1 0.2 - - - -
1036B LEU* 1.3 76.5 - - - +
1038B GLU* 1.3 57.0 + - + +
1040B GLY* 3.0 18.7 + - - -
1042B TYR* 3.6 34.3 - - + +
1043B ALA* 5.9 0.2 - - - -
1044B LYS* 3.0 39.5 + - - -
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Residues in contact with GLU1038 (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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1031B LEU* 5.7 2.3 - - - +
1034B GLN* 2.9 24.0 + - - +
1035B GLN* 2.9 26.6 + - - +
1037B GLU* 1.3 76.6 - - + +
1039B LYS* 1.3 61.2 + - + +
1040B GLY* 3.2 1.7 + - - -
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Residues in contact with LYS1039 (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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1035B GLN* 2.7 41.3 + - + +
1036B LEU* 3.7 14.9 - - + +
1037B GLU 3.3 0.2 - - - -
1038B GLU* 1.3 72.5 - - + +
1040B GLY* 1.3 61.8 + - - +
1041B ARG* 3.6 38.5 + - + +
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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