Contacts of the helix formed by residues 938 - 948 (chain A) in PDB entry 5XJY
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 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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936A GLY 3.2 2.2 - - - -
937A ALA* 1.3 79.8 - - - +
939A LYS* 1.3 54.0 + - - +
940A THR 3.4 1.8 - - - -
941A THR* 3.1 19.1 - - - -
942A THR* 2.5 33.5 + - - -
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Residues in contact with LYS 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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931A PHE* 5.7 8.3 - - + +
933A GLY* 3.5 29.8 - - - +
936A GLY 3.9 4.4 + - - +
937A ALA 3.7 1.0 - - - -
938A GLY* 1.3 75.1 - - - +
940A THR* 1.3 61.1 + - - +
942A THR* 2.9 22.0 + - - -
943A MET* 3.0 16.8 + - - +
1104A ILE* 5.4 7.4 - - + -
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Residues in contact with THR 940 (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 ALA 5.3 3.5 + - - -
938A GLY* 3.4 0.4 - - - -
939A LYS* 1.3 78.3 - - - +
941A THR* 1.3 58.1 + - - +
943A MET* 4.5 2.8 - - - +
944A SER* 2.8 34.5 + - - -
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Residues in contact with THR 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 ALA 5.1 1.3 + - - -
938A GLY* 3.1 22.3 + - - -
940A THR* 1.3 75.9 - - - +
942A THR* 1.3 54.2 + - - +
944A SER* 4.3 5.2 - - - -
945A ILE* 2.7 39.5 + - - +
954A SER* 6.3 2.9 - - - -
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Residues in contact with THR 942 (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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938A GLY 2.5 16.4 + - - -
939A LYS* 2.9 15.2 + - - -
941A THR* 1.3 75.1 - - - +
943A MET* 1.3 59.0 + - - +
945A ILE* 3.7 2.7 - - - +
946A LEU* 2.9 27.7 + - - +
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Residues in contact with MET 943 (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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939A LYS 3.0 13.4 + - - +
940A THR* 4.5 2.7 - - - +
942A THR* 1.3 74.6 - - - +
944A SER* 1.3 59.9 + - - +
946A LEU* 2.8 25.5 + - - +
947A THR* 3.0 16.3 + - - -
1055A ILE* 5.8 7.9 - - + +
1087A SER* 5.8 8.7 - - - -
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Residues in contact with SER 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 THR 2.8 23.2 + - - -
941A THR* 4.3 3.6 - - - -
943A MET* 1.3 77.2 - - - +
945A ILE* 1.3 56.9 + - - +
947A THR* 5.7 0.7 - - - -
948A GLY* 3.0 28.4 + - - +
950A PHE* 5.8 0.3 - - - +
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Residues in contact with ILE 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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941A THR* 2.7 25.2 + - - +
942A THR* 4.0 2.7 - - - +
944A SER* 1.3 76.1 - - - +
946A LEU* 1.3 63.4 + - - +
947A THR 3.3 1.2 + - - -
948A GLY 4.1 2.8 + - - +
950A PHE* 3.1 35.9 - - + +
951A PRO 5.4 0.3 - - - +
953A THR* 5.3 13.5 - - - -
954A SER* 5.7 4.0 - - - +
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Residues in contact with LEU 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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942A THR 2.9 18.6 + - - +
943A MET* 2.8 13.9 + - - +
945A ILE* 1.3 79.0 - - - +
947A THR* 1.3 57.1 + - - +
964A ILE* 5.2 9.2 - - - +
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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
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673A ILE* 4.9 14.5 - - - +
943A MET 3.0 10.9 + - - -
944A SER* 5.7 0.4 - - - -
945A ILE 4.7 0.4 - - - -
946A LEU* 1.3 80.8 - - - +
948A GLY* 1.3 65.2 + - - +
975A LEU 6.1 1.1 - - - -
977A VAL* 5.4 12.3 - - - -
1055A ILE* 5.9 6.7 - - - -
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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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673A ILE* 4.6 15.0 - - - -
944A SER* 3.0 23.3 + - - +
945A ILE 4.1 2.2 + - - -
946A LEU 3.9 0.8 - - - -
947A THR* 1.3 82.8 - - - +
949A LEU* 1.3 58.6 + - - -
950A PHE 3.3 9.9 + - - +
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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