Contacts of the helix formed by residues 79 - 92 (chain 4) in PDB entry 1LMB
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 SER 79 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104 GLU* 3.7 34.5 + - - +
144 ASP* 3.8 7.5 + - - -
774 SER* 3.5 7.6 + - - -
784 PRO* 1.3 81.5 - - - +
804 ILE* 1.3 65.9 + - - +
824 ARG* 3.3 8.7 + - - +
834 GLU* 3.0 21.3 + - - +
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Residues in contact with ILE 80 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144 ASP* 4.7 3.8 - - - +
574 LEU* 3.6 42.2 - - + +
584 ASN* 4.0 9.4 - - - +
594 ALA* 3.9 17.5 - - - -
624 ALA* 3.8 22.4 - - + -
734 VAL* 4.2 2.2 - - + -
774 SER* 3.1 20.6 + - - +
794 SER* 1.3 81.1 + - - +
814 ALA* 1.4 60.6 + - - +
834 GLU* 3.0 17.6 + - - +
844 ILE* 2.8 36.7 + - + +
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Residues in contact with ALA 81 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913 VAL* 4.1 16.2 - - + +
734 VAL* 3.8 7.8 - - + +
744 GLU* 3.4 39.5 - - + +
774 SER 3.1 13.9 + - - +
784 PRO 3.5 9.2 - - - +
794 SER 3.2 0.2 - - - -
804 ILE* 1.4 75.9 - - - +
824 ARG* 1.3 58.8 + - - +
844 ILE* 3.3 3.5 + - - +
854 TYR* 2.9 27.4 + - - +
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Residues in contact with ARG 82 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784 PRO 3.0 16.1 + - - +
794 SER* 3.9 7.2 - - - +
804 ILE 3.1 0.2 - - - -
814 ALA* 1.3 76.4 - - - +
834 GLU* 1.3 59.4 + - - +
854 TYR* 3.2 15.2 + - + +
864 GLU* 2.9 54.5 + - + +
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Residues in contact with GLU 83 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603 TYR* 3.7 36.2 - - + +
594 ALA* 4.2 24.8 + - - +
794 SER 3.0 13.4 + - - +
804 ILE* 3.0 22.0 + - - +
824 ARG* 1.3 77.3 - - - +
844 ILE* 1.4 61.9 + - - +
864 GLU* 3.3 13.2 + - - +
874 MET* 3.1 28.5 + - + +
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Residues in contact with ILE 84 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843 ILE* 4.8 2.8 - - + +
873 MET* 3.8 17.0 - - + +
883 TYR* 3.7 27.4 - - + +
913 VAL* 3.7 27.8 - - + -
594 ALA* 3.8 37.9 - - + +
634 ALA* 4.7 0.4 - - + -
734 VAL* 4.4 11.4 - - + -
804 ILE* 2.8 29.3 + - + +
814 ALA 3.6 3.8 - - - +
834 GLU* 1.4 73.4 - - - +
854 TYR* 1.3 64.5 + - - +
874 MET* 3.3 13.8 + - + +
884 TYR* 3.1 20.4 + - - +
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Residues in contact with TYR 85 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883 TYR* 3.6 32.8 - + + -
913 VAL* 4.8 4.3 - - + -
814 ALA 2.9 17.5 + - - +
824 ARG* 3.8 15.9 - - + +
844 ILE* 1.3 77.9 - - - +
864 GLU* 1.3 66.5 + - + +
884 TYR* 3.2 19.5 + + - +
894 GLU* 3.1 51.6 + - + +
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Residues in contact with GLU 86 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603 TYR* 5.0 10.4 + - + -
633 ALA* 5.4 0.2 - - - -
673 LYS* 2.8 32.9 + - - +
824 ARG* 2.9 56.0 + - + +
834 GLU* 3.3 11.2 + - - +
854 TYR* 1.3 82.1 - - + +
874 MET* 1.4 61.4 + - + +
894 GLU* 3.3 26.6 + - - +
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Residues in contact with MET 87 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593 ALA* 3.8 12.1 - - - -
603 TYR* 3.7 44.4 - - + -
633 ALA* 3.8 22.7 - - + -
843 ILE* 3.7 20.0 - - + +
873 MET* 3.3 28.5 - - + -
594 ALA* 4.2 10.5 - - + -
834 GLU* 3.1 19.2 + - - +
844 ILE* 3.7 30.1 - - + +
854 TYR 3.2 0.4 - - - -
864 GLU* 1.4 75.4 - - - +
884 TYR* 1.3 58.4 + - - +
904 ALA* 2.9 26.0 + - - +
914 VAL 3.7 2.8 + - - -
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Residues in contact with TYR 88 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843 ILE* 3.7 13.0 - - + +
853 TYR* 3.7 33.6 - + - -
883 TYR* 3.4 60.9 - + + -
844 ILE 3.1 13.1 + - - +
854 TYR* 3.2 20.2 - + - +
874 MET* 1.3 72.9 - - - +
894 GLU* 1.3 65.3 + - - +
904 ALA 3.0 2.0 - - - -
914 VAL* 3.0 19.1 + - + +
924 SER* 3.0 47.3 + - - -
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Residues in contact with GLU 89 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673 LYS* 3.0 30.1 + - - -
854 TYR* 3.1 48.1 + - + +
864 GLU* 3.3 20.9 - - - +
874 MET 3.2 0.4 - - - -
884 TYR* 1.3 78.4 - - - +
904 ALA* 1.4 57.8 + - - +
914 VAL 3.6 0.3 + - - -
924 SER* 3.9 21.0 + - - +
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Residues in contact with ALA 90 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633 ALA* 3.7 35.4 - - + +
663 ALA* 3.9 8.7 - - + -
673 LYS* 4.2 15.0 - - + +
713 VAL 4.2 2.1 - - - +
723 SER* 3.4 10.0 - - - -
733 VAL* 3.0 24.0 + - + -
864 GLU 3.9 0.8 + - - -
874 MET 2.9 14.1 + - - +
894 GLU* 1.4 76.6 - - - +
914 VAL* 1.3 60.5 + - - +
924 SER 4.6 1.3 - - - -
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Residues in contact with VAL 91 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723 SER* 3.3 2.9 + - - -
733 VAL* 4.1 4.3 - - + -
743 GLU* 2.7 36.9 - - - +
813 ALA* 4.0 22.4 - - + +
843 ILE* 3.8 36.6 - - + -
853 TYR* 5.0 4.7 - - + -
874 MET 4.2 0.2 - - - +
884 TYR* 3.0 35.7 + - + +
904 ALA* 1.3 77.5 - - - +
924 SER* 1.3 78.6 + - - +
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Residues in contact with SER 92 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723 SER* 4.4 6.9 + - - -
884 TYR* 3.0 38.1 + - - -
894 GLU* 3.9 16.1 - - - +
904 ALA 4.6 1.2 - - - -
914 VAL* 1.3 96.7 + - - +
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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