Contacts of the helix formed by residues 1025 - 1047 (chain B) in PDB entry 3LYI
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 ASN1025 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023B GLY 3.2 0.8 - - - -
1024B ARG* 1.3 85.0 - - - +
1026B SER* 1.3 62.6 + - - +
1027B SER* 3.1 21.0 + - - -
1028B ILE* 3.2 27.1 + - - +
1029B ARG* 3.2 34.6 + - - +
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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
----------------------------------------------------------
1025B ASN* 1.3 75.3 - - - +
1027B SER* 1.3 60.2 + - - +
1028B ILE 3.3 0.2 - - - -
1029B ARG* 3.8 21.4 + - - +
1030B LYS* 3.1 30.7 + - - +
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Residues in contact with SER1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025B ASN* 3.1 11.0 + - - -
1026B SER* 1.3 78.4 - - - +
1028B ILE* 1.3 63.6 + - - +
1030B LYS* 3.7 5.3 - - - +
1031B ALA* 3.3 21.5 + - - +
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Residues in contact with ILE1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941B PRO* 3.7 33.2 - - + -
1023B GLY* 4.0 10.1 - - - -
1024B ARG* 3.8 30.5 - - + -
1025B ASN* 3.2 23.8 + - - +
1027B SER* 1.3 76.4 - - - +
1029B ARG* 1.3 61.4 + - - +
1031B ALA* 3.1 7.4 + - - +
1032B VAL* 2.9 30.8 + - + +
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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
----------------------------------------------------------
1020B MET* 3.7 24.5 - - - +
1021B MET* 4.3 24.1 + - + +
1023B GLY* 3.2 36.8 + - - +
1024B ARG 4.4 1.8 + - - -
1025B ASN* 3.2 23.2 + - - +
1026B SER* 3.8 26.1 + - - +
1027B SER 3.5 0.2 - - - -
1028B ILE* 1.3 76.6 - - - +
1030B LYS* 1.3 58.1 + - - +
1032B VAL* 3.3 8.3 + - - +
1033B ARG* 2.9 31.3 + - - +
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Residues in contact with LYS1030 (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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1026B SER* 3.1 20.7 + - - +
1027B SER* 3.7 7.6 - - - +
1029B ARG* 1.3 77.1 - - - +
1031B ALA* 1.3 55.9 + - - +
1033B ARG* 3.4 9.3 + - - +
1034B ILE* 3.1 35.0 + - + +
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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
----------------------------------------------------------
943B TYR* 4.0 13.0 + - + +
1027B SER 3.3 11.0 + - - +
1028B ILE* 3.1 10.5 + - - +
1030B LYS* 1.3 75.4 - - - +
1032B VAL* 1.3 66.0 + - - +
1034B ILE* 3.4 11.5 + - - +
1035B ALA* 3.0 22.3 + - - +
1038B ARG* 5.6 0.7 + - - -
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Residues in contact with VAL1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B TRP* 3.8 32.3 - - + -
941B PRO* 4.4 15.7 - - + -
942B SER 4.2 10.1 - - - +
943B TYR* 4.0 24.2 - - + -
944B PRO* 4.1 3.3 - - + +
1019B LYS 4.7 1.6 - - - +
1020B MET* 4.2 18.2 - - + +
1023B GLY* 5.8 2.5 - - - +
1028B ILE* 2.9 21.8 + - + +
1029B ARG* 3.6 9.9 - - - +
1031B ALA* 1.3 74.6 - - + +
1033B ARG* 1.3 52.8 + - - +
1035B ALA* 3.1 8.8 + - - +
1036B PHE* 2.7 33.6 + - - +
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Residues in contact with ARG1033 (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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1017B LYS* 4.4 13.7 - - - +
1020B MET* 3.9 29.3 - - + +
1029B ARG 2.9 17.1 + - - +
1030B LYS* 3.5 10.1 - - - +
1031B ALA 3.3 0.2 - - - -
1032B VAL* 1.3 77.7 - - - +
1034B ILE* 1.3 59.1 + - + +
1036B PHE* 3.3 28.1 + - - +
1037B ASP* 2.8 52.9 + - - +
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Residues in contact with ILE1034 (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 LYS* 3.1 22.7 + - + +
1031B ALA* 3.7 12.6 - - + +
1032B VAL 3.3 0.2 - - - -
1033B ARG* 1.3 76.0 - - + +
1035B ALA* 1.3 60.0 + - - +
1037B ASP* 3.1 11.8 + - + +
1038B ARG* 3.0 50.1 + - + +
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Residues in contact with ALA1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943B TYR* 3.5 30.5 - - + +
944B PRO* 3.8 12.3 - - + +
992B PHE* 3.4 27.3 - - + +
1031B ALA 3.0 8.7 + - - +
1032B VAL 3.4 7.6 - - - +
1034B ILE* 1.3 76.6 - - - +
1036B PHE* 1.3 57.0 + - - +
1038B ARG* 3.3 9.5 + - - +
1039B ALA* 3.0 27.7 + - - +
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Residues in contact with PHE1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B TRP* 3.5 24.2 - + + -
944B PRO* 3.6 11.1 - - + +
1009B LEU* 3.8 21.5 - - + -
1016B ASP* 3.7 33.4 - - + -
1017B LYS* 6.2 0.2 - - + -
1020B MET* 3.8 26.0 - - + -
1032B VAL 2.7 19.8 + - - +
1033B ARG* 3.3 33.7 - - - +
1035B ALA* 1.3 68.6 - - - +
1037B ASP* 1.3 62.3 + - - +
1039B ALA* 3.3 2.2 + - - +
1040B MET* 2.9 56.1 + - + +
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Residues in contact with ASP1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033B ARG* 2.8 49.1 + - - +
1034B ILE* 3.1 13.5 + - + +
1036B PHE* 1.3 77.3 - - - +
1038B ARG* 1.3 61.7 + - + +
1040B MET* 3.4 6.5 + - - +
1041B ASN* 3.0 31.7 + - - +
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Residues in contact with ARG1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943B TYR* 4.6 1.6 + - - -
992B PHE* 2.8 45.8 + - + +
993B ASP* 3.8 12.1 - - - +
994B ASN* 3.3 32.3 + - - +
996B ARG* 5.9 5.3 - - - +
1031B ALA 5.6 0.4 + - - -
1034B ILE* 3.0 31.7 + - + +
1035B ALA* 3.7 14.4 - - - +
1036B PHE 3.3 0.2 - - - -
1037B ASP* 1.3 75.9 - - + +
1039B ALA* 1.3 57.6 + - - +
1041B ASN* 3.2 10.7 + - - +
1042B HIS* 3.0 26.9 + - - +
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Residues in contact with ALA1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B VAL* 4.0 6.0 - - + +
944B PRO* 4.0 9.6 - - + -
992B PHE* 3.7 33.1 - - + -
1009B LEU* 3.9 18.4 - - + -
1035B ALA 3.0 17.0 + - - +
1036B PHE 3.7 4.9 - - - +
1038B ARG* 1.3 73.9 - - - +
1040B MET* 1.3 63.9 + - - +
1042B HIS* 3.2 4.5 - - - +
1043B LEU* 3.1 24.6 + - - +
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Residues in contact with MET1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009B LEU* 3.4 16.8 - - + -
1010B GLY* 3.5 22.9 - - - +
1036B PHE* 2.9 50.6 + - + +
1037B ASP* 3.8 7.4 - - - +
1039B ALA* 1.3 73.9 - - - +
1041B ASN* 1.3 66.5 + - - +
1043B LEU* 3.3 44.9 + - + +
1044B SER* 3.5 15.2 + - - -
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Residues in contact with ASN1041 (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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1037B ASP* 3.0 20.5 + - - +
1038B ARG* 3.2 12.4 + - - +
1040B MET* 1.3 77.2 - - - +
1042B HIS* 1.3 66.2 + - - +
1044B SER* 3.2 9.5 + - - -
1045B ARG* 3.0 24.4 + - - +
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Residues in contact with HIS1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LYS* 5.4 1.6 - - - +
932B VAL* 3.6 24.0 - - + +
946B LEU* 3.5 36.6 - - + +
992B PHE* 3.7 22.0 - + + -
1038B ARG 3.0 12.4 + - - +
1039B ALA 3.2 11.0 - - - +
1041B ASN* 1.3 76.3 - - - +
1043B LEU* 1.3 61.1 + - - +
1045B ARG* 3.3 12.7 + - - +
1046B VAL* 3.3 42.8 + - + +
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Residues in contact with LEU1043 (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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931B LYS* 6.0 1.3 - - + -
932B VAL* 3.8 31.2 - - + +
1009B LEU 3.7 17.7 - - - +
1010B GLY* 4.6 5.4 - - - +
1011B ILE* 5.4 5.8 - - + -
1039B ALA 3.1 9.1 + - - +
1040B MET* 3.3 35.9 - - + +
1041B ASN 3.2 0.6 - - - -
1042B HIS* 1.3 76.2 - - - +
1044B SER* 1.3 61.6 + - - +
1046B VAL* 3.6 11.6 - - + +
1047B HIS* 3.4 24.3 + - - +
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Residues in contact with SER1044 (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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1040B MET 3.5 11.2 + - - -
1041B ASN* 3.2 11.4 + - - -
1043B LEU* 1.3 77.5 - - - +
1045B ARG* 1.3 58.5 + - - +
1046B VAL 3.1 1.3 - - - -
1047B HIS* 3.1 21.6 + - - -
1048B GLY* 3.4 10.9 + - - -
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Residues in contact with ARG1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B ASN 3.0 17.1 + - - +
1042B HIS* 3.3 6.9 + - - +
1044B SER* 1.3 76.1 - - - +
1046B VAL* 1.3 60.2 + - + +
1048B GLY* 4.4 6.1 + - - -
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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
----------------------------------------------------------
932B VAL* 6.1 0.2 - - + -
1042B HIS* 3.3 43.1 - - + +
1043B LEU* 3.6 17.5 - - + +
1045B ARG* 1.3 79.9 - - + +
1047B HIS* 1.3 60.9 + - + +
1048B GLY 3.2 7.1 + - - -
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Residues in contact with HIS1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B LEU 3.4 18.0 + - - +
1044B SER* 3.1 9.0 + - - +
1046B VAL* 1.3 77.0 - - + +
1048B GLY* 1.3 58.3 + - - +
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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