Contacts of the helix formed by residues 938 - 951 (chain A) in PDB entry 3LMG
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 THR 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807A GLU* 4.7 11.0 - - - +
875A VAL* 4.9 2.7 - - - -
936A ARG 5.0 3.4 - - - +
937A PRO* 1.3 77.6 - - - +
939A PHE* 1.3 64.4 + - - +
940A LYS* 3.5 16.0 - - + +
941A GLU* 2.9 38.3 + - - +
942A LEU* 3.1 22.5 + - - +
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Residues in contact with PHE 939 (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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800A ALA* 3.9 20.0 - - - +
803A MET* 3.5 58.8 - - + -
804A TYR* 4.0 14.0 - - + +
807A GLU* 3.6 25.3 + - + +
871A HIS* 3.8 12.8 - - + -
874A ASP 4.0 2.0 - - - -
875A VAL* 3.7 37.0 - - + -
878A TYR* 3.8 30.1 - + + -
938A THR* 1.3 70.6 - - - +
940A LYS* 1.3 64.4 + - - +
942A LEU* 3.8 14.4 - - + +
943A ALA* 3.0 24.8 + - - +
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Residues in contact with LYS 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A TYR* 3.3 46.8 + - + -
807A GLU* 5.7 3.6 - - - +
938A THR* 3.5 14.6 - - + +
939A PHE* 1.3 81.2 - - - +
941A GLU* 1.3 63.8 + - + +
943A ALA* 3.2 5.3 + - - +
944A ASN* 3.2 29.8 + - - +
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Residues in contact with GLU 941 (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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937A PRO* 3.4 15.6 - - + +
938A THR* 2.9 40.5 + - - +
940A LYS* 1.3 81.4 - - + +
942A LEU* 1.3 58.5 + - - +
944A ASN* 3.1 16.1 + - - +
945A GLU* 2.9 30.5 + - - +
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Residues in contact with LEU 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A ALA* 4.3 6.2 - - + +
875A VAL* 4.2 20.4 - - + -
878A TYR* 3.7 36.5 + - + -
924A VAL* 3.8 28.5 - - + +
928A CYS* 4.2 4.9 - - - -
937A PRO* 3.7 22.4 - - + -
938A THR 3.1 20.0 + - - +
939A PHE* 3.8 23.3 - - + +
940A LYS 3.2 0.2 - - - -
941A GLU* 1.3 73.6 - - - +
943A ALA* 1.3 65.2 + - - +
945A GLU* 4.3 3.5 - - + +
946A PHE* 3.3 31.0 + - - +
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Residues in contact with ALA 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A VAL* 4.0 11.7 - - + +
800A ALA* 3.9 16.5 - - + +
801A LYS* 4.7 19.7 - - + +
804A TYR* 6.1 1.3 - - + -
939A PHE 3.0 14.3 + - - +
940A LYS* 3.2 11.4 + - - +
942A LEU* 1.3 76.5 - - - +
944A ASN* 1.3 64.0 + - - +
946A PHE* 4.5 0.2 - - - -
947A THR* 3.3 27.0 + - - +
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Residues in contact with ASN 944 (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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940A LYS* 3.2 20.2 + - - +
941A GLU* 3.1 19.0 + - - +
943A ALA* 1.3 80.8 - - - +
945A GLU* 1.3 58.7 + - - +
947A THR* 3.2 11.1 - - - +
948A ARG* 2.9 32.4 + - - +
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Residues in contact with GLU 945 (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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920A ASP 5.6 0.4 - - - -
924A VAL* 3.6 31.2 - - + +
941A GLU 2.9 14.7 + - - +
942A LEU* 3.7 6.0 + - + +
943A ALA 3.6 0.2 - - - -
944A ASN* 1.3 76.0 - - - +
946A PHE* 1.3 63.5 + - + +
948A ARG* 2.7 48.2 + - - +
949A MET* 3.2 42.3 + - + +
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Residues in contact with PHE 946 (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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793A LEU* 3.7 31.9 - - + +
796A GLY* 4.3 9.2 - - - -
797A VAL* 3.6 21.1 - - + +
878A TYR* 3.6 24.0 - + - -
882A VAL* 3.7 26.9 - - + -
886A MET* 3.9 23.1 - - + -
921A VAL* 4.4 10.3 - - + -
924A VAL* 3.6 31.9 - - + -
942A LEU* 3.3 24.9 + - + +
943A ALA 4.6 0.2 - - - +
944A ASN 3.3 0.6 - - - -
945A GLU* 1.3 78.7 - - + +
947A THR* 1.3 59.5 + - - +
949A MET* 3.2 10.3 + - - +
950A ALA* 2.8 27.9 + - - +
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Residues in contact with THR 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A VAL* 3.8 17.5 - - - +
801A LYS* 6.0 0.6 - - - -
943A ALA 3.3 17.1 + - - +
944A ASN* 3.2 19.7 - - - +
946A PHE* 1.3 78.7 - - - +
948A ARG* 1.3 63.5 + - - +
950A ALA* 3.3 17.7 + - - +
951A ARG* 3.3 38.3 + - - +
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Residues in contact with ARG 948 (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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920A ASP* 4.9 10.5 + - - -
944A ASN 2.9 18.7 + - - +
945A GLU* 2.7 38.9 + - - +
947A THR* 1.3 80.1 - - + +
949A MET* 1.3 61.2 + - - +
951A ARG* 3.3 27.1 - - + +
952A ASP 4.5 0.3 + - - -
955A ARG* 6.1 1.2 - - - +
956A TYR* 4.4 27.4 + - - +
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Residues in contact with MET 949 (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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793A LEU* 3.8 11.3 - - + +
920A ASP* 3.6 35.4 - - + +
921A VAL* 3.7 25.6 - - + -
924A VAL* 4.1 3.1 - - + -
945A GLU* 3.2 44.6 + - + +
946A PHE* 3.2 17.2 + - - +
948A ARG* 1.3 74.4 - - + +
950A ALA* 1.3 63.1 + - - +
951A ARG 3.1 3.2 + - - -
952A ASP 3.1 26.7 + - - +
953A PRO* 3.6 3.5 - - - +
956A TYR* 3.5 41.8 - - + -
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Residues in contact with ALA 950 (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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790A GLN* 2.9 28.4 + - - +
793A LEU* 4.1 18.8 - - + +
794A ASN* 4.3 17.5 - - - +
797A VAL* 4.8 4.3 - - + -
946A PHE 2.8 16.0 + - - +
947A THR* 3.5 15.7 - - - +
948A ARG 3.3 0.4 - - - -
949A MET* 1.3 75.1 - - - +
951A ARG* 1.3 64.8 + - - +
953A PRO* 3.5 2.0 - - - +
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Residues in contact with ARG 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A THR* 3.3 38.2 + - - +
948A ARG* 3.3 19.1 - - + +
949A MET 3.1 0.4 - - - -
950A ALA* 1.3 78.5 - - - +
952A ASP* 1.3 58.1 + - + +
953A PRO* 3.4 7.3 - - - +
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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
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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