Contacts of the helix formed by residues 1025 - 1046 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A ARG* 1.3 79.4 - - - +
1026A SER* 1.3 65.5 + - - +
1027A SER* 3.0 14.1 + - - -
1028A ILE* 2.9 37.1 + - - +
1029A ARG* 3.1 32.8 + - - +
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Residues in contact with SER1026 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025A ASN* 1.3 77.3 - - - +
1027A SER* 1.3 61.2 + - - +
1029A ARG* 3.3 24.2 + - - +
1030A LYS* 2.9 58.8 + - - +
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Residues in contact with SER1027 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A ASN* 3.0 14.3 + - - -
1026A SER* 1.3 83.9 + - - +
1028A ILE* 1.3 64.9 + - - +
1030A LYS* 3.5 13.5 + - - +
1031A ALA* 3.2 22.0 + - - +
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Residues in contact with ILE1028 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A PRO* 3.8 25.4 - - + -
1023A GLY* 3.8 19.7 - - - -
1024A ARG* 3.9 27.6 - - + +
1025A ASN* 2.9 30.2 + - - +
1027A SER* 1.3 77.9 - - - +
1029A ARG* 1.3 64.8 + - - +
1031A ALA* 3.3 7.2 + - - +
1032A VAL* 3.0 25.0 + - + +
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Residues in contact with ARG1029 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020A MET* 3.6 25.8 - - - +
1021A MET* 3.7 32.9 + - + +
1023A GLY* 2.9 38.6 + - - +
1024A ARG 4.1 2.4 + - - -
1025A ASN* 3.1 26.5 + - - +
1026A SER* 3.5 27.8 - - - +
1027A SER 3.2 0.2 - - - -
1028A ILE* 1.3 77.0 - - - +
1030A LYS* 1.3 57.6 + - + +
1032A VAL* 3.3 6.5 + - - +
1033A ARG* 2.9 30.7 + - - +
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Residues in contact with LYS1030 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026A SER* 2.9 51.5 + - - +
1027A SER* 3.8 12.9 + - - +
1029A ARG* 1.3 74.4 - - + +
1031A ALA* 1.3 56.4 + - - +
1033A ARG* 3.2 30.3 + - - +
1034A ILE* 3.0 39.4 + - + +
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Residues in contact with ALA1031 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A TYR* 3.8 12.9 + - + +
994A ASN* 5.8 3.8 - - - +
1027A SER 3.2 14.0 + - - +
1028A ILE* 3.7 9.6 - - - +
1030A LYS* 1.3 73.2 - - - +
1032A VAL* 1.3 65.6 + - + +
1034A ILE* 3.5 11.1 + - - +
1035A ALA* 3.2 20.6 + - - +
1038A ARG* 5.1 0.9 + - - -
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Residues in contact with VAL1032 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A TRP* 3.7 32.8 - - + -
941A PRO* 4.2 21.3 - - + -
942A SER 4.2 5.4 - - - +
943A TYR* 3.9 27.1 - - + -
944A PRO* 4.1 2.5 - - + +
1019A LYS 4.8 2.2 - - - +
1020A MET* 4.3 16.8 - - + +
1023A GLY* 5.7 2.5 - - - +
1028A ILE* 3.0 23.1 + - + +
1029A ARG* 3.6 6.5 - - - +
1031A ALA* 1.3 73.6 - - + +
1033A ARG* 1.3 61.5 + - - +
1035A ALA* 3.2 4.2 + - - +
1036A PHE* 2.8 26.3 + - - +
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Residues in contact with ARG1033 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020A MET* 4.3 26.9 - - + +
1029A ARG 2.9 16.9 + - - +
1030A LYS* 3.2 36.8 + - - +
1032A VAL* 1.3 78.3 - - - +
1034A ILE* 1.3 72.0 + - - +
1036A PHE* 3.2 2.8 + - + +
1037A ASP* 3.0 38.9 + - - +
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Residues in contact with ILE1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030A LYS* 3.0 27.3 + - + +
1031A ALA* 3.8 8.5 - - - +
1033A ARG* 1.3 89.7 - - - +
1035A ALA* 1.3 55.3 + - - +
1037A ASP* 3.3 11.6 + - - +
1038A ARG* 3.0 60.2 + - + +
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Residues in contact with ALA1035 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943A TYR* 3.3 41.1 - - + +
944A PRO* 3.7 10.7 - - + +
992A PHE* 3.5 20.6 - - + +
1031A ALA 3.2 5.7 + - - +
1032A VAL 3.2 8.8 + - - +
1034A ILE* 1.3 72.5 - - - +
1036A PHE* 1.3 61.1 + - - +
1038A ARG* 3.2 7.5 + - - +
1039A ALA* 2.9 29.1 + - - +
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Residues in contact with PHE1036 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A TRP* 3.7 20.6 - + + -
944A PRO* 3.5 13.2 - - + +
1009A LEU* 4.0 12.1 - - + -
1016A ASP* 3.5 37.7 - - + -
1020A MET* 3.9 29.8 - - + -
1032A VAL 2.8 13.4 + - - +
1033A ARG* 3.2 8.0 + - + +
1035A ALA* 1.3 76.5 - - - +
1037A ASP* 1.3 65.4 + - - +
1039A ALA* 3.1 3.5 + - - +
1040A MET* 2.8 68.1 + - + +
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Residues in contact with ASP1037 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A ARG* 3.0 31.7 + - - +
1034A ILE* 3.4 11.8 - - - +
1036A PHE* 1.3 93.4 - - - +
1038A ARG* 1.3 55.4 + - - +
1040A MET* 3.5 5.8 + - - +
1041A ASN* 3.0 37.1 + - - +
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Residues in contact with ARG1038 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A TYR* 4.4 1.8 + - - -
992A PHE* 2.8 51.6 + - + -
993A ASP* 4.0 10.7 - - - +
994A ASN* 3.0 34.6 + - - +
996A ARG* 6.2 2.0 - - - +
1031A ALA 5.1 1.0 + - - -
1034A ILE* 3.0 45.2 + - + +
1035A ALA* 3.5 15.6 - - - +
1037A ASP* 1.3 76.8 - - - +
1039A ALA* 1.3 56.8 + - - +
1041A ASN* 3.4 10.7 + - - +
1042A HIS* 3.0 26.2 + - - +
1045A ARG* 4.6 4.2 + - - +
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Residues in contact with ALA1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A VAL* 4.0 4.5 - - + +
944A PRO* 3.9 11.2 - - + -
992A PHE* 3.5 38.0 - - + -
1009A LEU* 3.9 15.9 - - + -
1035A ALA 2.9 14.4 + - - +
1036A PHE 3.5 6.3 - - - +
1038A ARG* 1.3 73.9 - - - +
1040A MET* 1.3 58.6 + - - +
1042A HIS* 3.1 4.5 + - - +
1043A LEU* 3.0 32.9 + - - +
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Residues in contact with MET1040 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A LEU* 3.7 9.4 - - - -
1010A GLY* 3.6 37.5 - - - +
1016A ASP* 5.4 0.2 - - - +
1036A PHE* 2.8 54.1 + - + +
1037A ASP* 3.9 7.2 - - - +
1038A ARG 3.3 0.2 - - - -
1039A ALA* 1.3 68.9 - - - +
1041A ASN* 1.3 62.4 + - - +
1043A LEU* 3.2 13.8 + - + +
1044A SER* 2.8 33.4 + - - +
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Residues in contact with ASN1041 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037A ASP* 3.0 26.1 + - - +
1038A ARG* 3.6 9.3 - - - +
1040A MET* 1.3 76.1 - - - +
1042A HIS* 1.3 61.5 + - - +
1044A SER* 3.2 11.0 + - - -
1045A ARG* 3.0 44.6 + - - +
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Residues in contact with HIS1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931A LYS* 5.9 0.6 - - - +
932A VAL* 3.6 24.7 - - + +
946A LEU* 3.7 33.3 - - + +
961A GLY* 5.1 9.0 - - - -
963A THR 5.8 2.7 - - - -
964A ILE* 6.6 0.2 - - + -
992A PHE* 3.9 20.5 - + + -
1038A ARG 3.0 14.8 + - - +
1039A ALA 3.3 7.9 - - - +
1041A ASN* 1.3 74.7 - - - +
1043A LEU* 1.3 67.9 + - + +
1045A ARG* 3.0 35.2 + - - +
1046A VAL* 3.2 35.9 + - + +
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Residues in contact with LEU1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A VAL* 3.6 38.1 - - + -
1009A LEU* 3.8 31.6 - - + +
1010A GLY* 4.4 3.8 - - - +
1011A ILE* 6.3 1.6 - - + -
1039A ALA 3.0 14.5 + - - +
1040A MET* 3.2 22.4 + - + +
1042A HIS* 1.3 75.4 - - - +
1044A SER* 1.3 63.2 + - - +
1046A VAL* 3.3 17.0 + - + +
1047A HIS* 3.2 22.2 + - - +
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Residues in contact with SER1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040A MET* 2.8 19.1 + - - +
1041A ASN* 3.2 15.1 + - - -
1043A LEU* 1.3 74.7 - - - +
1045A ARG* 1.3 61.8 + - - +
1047A HIS* 3.3 21.5 + - - +
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Residues in contact with ARG1045 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038A ARG* 4.6 3.8 + - - +
1041A ASN* 3.0 39.4 + - + +
1042A HIS* 3.0 36.6 + - - +
1044A SER* 1.3 77.1 - - - +
1046A VAL* 1.3 62.4 + - + +
1047A HIS 3.8 2.5 + - - +
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Residues in contact with VAL1046 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A VAL* 6.1 0.2 - - + -
959A HIS* 3.1 48.7 + - + +
960A ASN 4.2 2.2 - - - -
961A GLY* 3.8 32.1 - - - +
1042A HIS* 3.6 30.5 - - + +
1043A LEU* 3.3 27.1 - - + +
1045A ARG* 1.3 81.6 - - + +
1047A HIS* 1.3 60.8 + - - +
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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