Contacts of the helix formed by residues 947 - 959 (chain A) in PDB entry 3UGM
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 GLY 947 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912A ILE 3.9 8.3 + - - -
913A GLY* 5.7 0.4 - - - -
945A ASN 3.2 0.4 + - - -
946A ILE* 1.3 84.3 - - - +
948A GLY* 1.3 64.1 + - - +
949A LYS 3.3 1.8 - - - -
950A GLN* 3.5 8.9 + - - +
951A ALA* 3.1 20.1 + - - +
982A GLY* 5.8 0.3 - - - -
983A LYS 5.6 0.2 + - - -
19B C 3.8 34.7 + - - -
20B A 4.0 4.3 + - - -
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Residues in contact with GLY 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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917A ALA* 5.4 3.7 - - - +
942A ILE 3.8 14.8 - - - -
943A ALA* 3.8 20.4 - - - -
945A ASN* 3.0 16.1 + - - -
946A ILE 4.4 0.2 - - - -
947A GLY* 1.3 74.3 - - - +
949A LYS* 1.3 71.9 + - - +
951A ALA* 2.8 3.9 + - - -
952A LEU* 2.8 23.3 + - - +
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Residues in contact with LYS 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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916A GLN* 3.2 52.5 - - + +
917A ALA* 4.3 9.4 - - - +
920A THR* 2.8 38.7 + - + +
947A GLY* 4.3 0.2 - - - -
948A GLY* 1.3 76.7 - - - +
950A GLN* 1.3 73.8 + - - +
952A LEU* 3.4 5.4 + - - +
953A GLU* 3.1 47.9 + - - +
19B C 3.3 17.7 + - - +
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Residues in contact with GLN 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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947A GLY 3.7 7.9 - - - +
948A GLY 3.2 0.4 - - - -
949A LYS* 1.3 92.9 + - - +
951A ALA* 1.3 65.2 + - - +
953A GLU* 3.2 15.9 + - - +
954A THR* 3.1 20.3 + - - -
983A LYS* 3.2 41.9 + - + +
19B C 2.8 46.3 + - - +
20B A 3.8 20.2 - - - +
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Residues in contact with ALA 951 (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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942A ILE* 3.8 16.4 - - + +
945A ASN* 6.4 0.2 - - + -
947A GLY 3.1 10.0 + - - +
948A GLY* 2.8 12.7 + - - +
950A GLN* 1.3 75.9 - - - +
952A LEU* 1.3 65.5 + - - +
954A THR* 3.6 2.4 + - - -
955A VAL* 3.3 22.3 + - - +
977A ALA* 3.5 23.3 - - + +
979A ASN 5.3 2.7 - - - +
982A GLY* 4.0 12.3 - - - -
983A LYS* 3.6 14.4 - - - +
986A LEU* 4.7 1.7 - - - +
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Residues in contact with LEU 952 (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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917A ALA 4.8 1.6 - - - +
920A THR* 4.0 18.4 - - + +
921A VAL* 3.8 40.2 - - + +
924A LEU* 5.0 10.3 - - + -
934A LEU* 6.0 0.4 - - + -
939A VAL* 3.9 32.8 - - + +
942A ILE* 3.7 22.6 - - + +
943A ALA* 4.1 11.2 - - + -
948A GLY 2.8 15.2 + - - +
949A LYS* 3.4 9.4 - - - +
951A ALA* 1.3 71.2 - - - +
953A GLU* 1.3 69.0 + - - +
955A VAL* 3.0 14.8 + - + +
956A GLN* 3.0 13.0 + - - +
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Residues in contact with GLU 953 (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 THR* 4.4 13.3 - - + +
924A LEU* 4.7 8.0 - - + +
949A LYS* 3.1 41.6 + - - +
950A GLN* 3.2 15.8 + - - +
952A LEU* 1.3 76.8 - - - +
954A THR* 1.3 55.4 + - - +
955A VAL 2.6 13.5 + - - -
956A GLN* 2.8 23.5 + - + +
957A ARG* 2.9 22.5 + - - +
983A LYS* 5.8 1.1 + - + -
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Residues in contact with THR 954 (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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950A GLN 3.1 6.4 + - - -
951A ALA 4.2 0.7 - - - -
953A GLU* 1.3 75.0 - - - +
955A VAL* 1.3 52.6 + - - +
957A ARG* 3.3 25.0 + - - +
958A LEU* 2.8 54.1 + - + +
983A LYS* 2.6 53.4 - - - +
986A LEU* 3.6 23.6 - - + +
987A GLU* 4.1 1.1 - - + -
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Residues in contact with VAL 955 (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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934A LEU* 4.7 21.8 - - + -
942A ILE* 4.5 12.3 - - + -
951A ALA 3.3 16.4 + - - +
952A LEU* 3.0 10.2 + - + +
953A GLU 2.6 5.1 + - - -
954A THR* 1.3 68.8 - - - +
956A GLN* 1.3 71.2 + - - +
957A ARG 2.6 2.8 + - - -
958A LEU 3.2 0.6 + - - -
959A LEU* 2.7 41.9 + - + +
973A VAL* 4.9 13.9 - - + -
974A VAL* 5.6 1.8 - - + -
977A ALA* 3.7 26.5 - - + -
986A LEU* 3.8 9.0 - - + -
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Residues in contact with GLN 956 (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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924A LEU* 3.8 35.0 - - + +
927A VAL* 4.5 20.4 - - - +
952A LEU 3.0 6.9 + - - +
953A GLU* 2.8 11.7 + - + +
955A VAL* 1.3 78.6 - - - +
957A ARG* 1.3 65.0 + - + +
959A LEU* 3.7 21.5 - - - +
960A PRO* 4.7 0.7 - - - +
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Residues in contact with ARG 957 (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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953A GLU* 2.9 22.6 + - - +
954A THR* 3.3 36.5 + - - +
955A VAL 2.6 4.4 + - - -
956A GLN* 1.3 76.4 - - + +
958A LEU* 1.3 73.9 + - + +
959A LEU 3.0 8.2 + - - -
960A PRO* 3.4 14.2 - - - +
961A VAL* 4.7 2.4 - - - +
983A LYS* 5.0 4.0 - - - +
987A GLU* 2.6 36.6 + - - +
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Residues in contact with LEU 958 (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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954A THR* 2.8 40.3 + - + +
955A VAL* 3.5 2.5 - - - -
957A ARG* 1.3 88.7 - - + +
959A LEU* 1.3 60.2 + - - +
960A PRO* 3.6 1.3 - - - -
961A VAL* 3.8 25.8 - - + -
962A LEU* 2.8 37.1 - - + +
973A VAL* 5.5 3.2 - - - +
986A LEU* 5.0 7.2 - - + +
987A GLU* 3.8 29.2 - - + +
990A GLN* 5.3 11.7 - - + -
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Residues in contact with LEU 959 (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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933A GLY 6.3 1.3 - - - +
934A LEU* 5.9 8.3 - - + -
955A VAL* 2.7 30.5 + - + +
956A GLN* 3.7 18.6 - - - +
958A LEU* 1.3 80.5 - - - +
960A PRO* 1.3 76.2 - - + +
962A LEU* 3.7 7.4 + - - +
963A CYS* 4.0 15.2 + - - +
970A PRO* 6.1 7.4 - - + -
973A VAL* 5.4 10.2 - - + +
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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