Contacts of the helix formed by residues 46 - 53 (chain B) in PDB entry 1GXD
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 LYS 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LEU* 6.0 1.3 - - + -
42B LYS* 3.5 47.4 - - - +
43B ASP 4.2 5.8 - - - +
44B THR 4.1 6.3 - - - +
45B LEU* 1.3 81.3 - - - +
47B LYS* 1.3 61.2 + - + +
48B MET 3.2 1.3 - - - +
49B GLN* 3.6 8.9 - - - +
50B LYS* 2.7 35.3 + - - +
56B GLN* 4.0 34.0 - - + +
57B THR 4.8 2.5 - - - -
58B GLY* 3.8 22.0 - - - +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 4.3 13.2 - - + -
43B ASP* 3.8 21.4 + - - +
44B THR* 4.6 6.5 - - + +
45B LEU 3.9 0.6 - - - +
46B LYS* 1.3 82.0 - - - +
48B MET* 1.3 62.7 + - - +
50B LYS* 3.3 12.9 + - + +
51B PHE* 2.9 22.3 + - - +
78B VAL* 4.5 18.9 - - + +
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 3.7 17.5 - - + +
25B LEU* 3.9 22.0 - - + -
29B TYR* 3.4 41.5 - - + +
45B LEU* 4.1 12.0 - - - +
46B LYS 3.7 0.8 - - - +
47B LYS* 1.3 77.5 - - - +
49B GLN* 1.3 72.1 + - - +
51B PHE* 2.9 18.9 + - - +
52B PHE* 3.2 38.6 + - + -
54B LEU* 5.2 1.6 - - + -
64B THR* 3.6 20.4 - - - +
67B THR* 4.5 10.8 - - - -
68B MET* 3.7 22.0 - - + +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.3 32.2 + - - +
46B LYS* 3.3 5.1 + - - +
48B MET* 1.3 81.7 - - - +
50B LYS* 1.3 52.0 + - - +
52B PHE* 3.0 4.3 + - - +
53B GLY 2.7 32.1 + - - -
54B LEU* 3.4 19.3 + - + +
55B PRO 3.0 25.4 + - - +
56B GLN* 3.2 8.2 - - + -
57B THR 3.0 16.8 + - - -
58B GLY 3.1 9.3 + - - -
60B LEU* 3.4 28.5 - - - +
64B THR* 3.5 23.4 + - - +
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS 2.7 22.7 + - - +
47B LYS* 3.4 12.3 - - + +
49B GLN* 1.3 70.6 - - - +
51B PHE* 1.3 66.3 + - - +
53B GLY* 2.9 15.9 + - - +
54B LEU 5.0 0.9 - - - +
56B GLN* 3.4 33.3 - - - +
386B GLN* 3.4 15.3 + - - +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 3.8 12.6 - + + +
47B LYS 2.9 13.6 + - - +
48B MET 2.9 10.7 + - - +
50B LYS* 1.3 77.2 - - - +
52B PHE* 1.3 85.4 + + - +
77B ASP* 3.6 47.1 - - + -
384B HIS* 4.3 15.3 - - + -
385B SER 3.7 27.4 - - - -
386B GLN* 3.0 49.0 + - + +
394B PRO* 4.4 5.6 - - + -
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 3.4 7.6 - + - -
29B TYR* 3.7 14.6 - - - -
48B MET* 3.2 50.8 + - + -
49B GLN 3.0 5.5 + - - +
51B PHE* 1.3 89.2 - + - +
53B GLY* 1.3 65.7 + - - +
54B LEU* 4.4 12.8 - - + -
67B THR* 4.3 16.4 - - + -
72B ARG* 3.4 25.1 - - - -
77B ASP* 3.6 6.1 - - - -
386B GLN 5.6 1.1 - - - +
388B PRO* 5.8 4.2 - - - +
394B PRO* 4.1 10.5 - - + -
395B ILE* 4.0 23.8 - - + -
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Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLN 2.7 6.7 + - - -
50B LYS* 2.9 14.4 + - - -
52B PHE* 1.3 84.6 - - - +
54B LEU* 1.3 69.4 + - - +
475B MET* 4.1 14.9 - - - +
476B GLY 5.5 0.2 - - - +
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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