Contacts of the helix formed by residues 38 - 46 (chain D) in PDB entry 1GUM
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 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D THR* 1.3 75.4 - - + +
39D GLU* 1.3 53.2 + - + +
41D LEU* 2.8 8.6 - - + +
42D TYR* 2.6 69.8 + - + +
218D ASN 4.2 11.8 + - - +
219D ILE* 3.5 29.4 - - - +
220D PHE* 3.5 25.1 + - - +
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Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D THR* 3.0 13.1 - - + +
38D LYS* 1.3 80.5 - - + +
40D GLN* 1.3 72.8 + - - +
42D TYR* 2.7 32.8 + - + +
43D LYS* 2.8 41.0 + - + +
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Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLU* 5.8 2.4 + - - -
34D PHE 3.6 14.5 + - - -
35D LEU* 4.0 13.2 - - + +
36D GLU* 2.5 47.2 + - - +
37D THR* 2.9 27.2 + - - +
39D GLU* 1.3 81.2 + - - +
41D LEU* 1.3 62.1 + - - +
43D LYS* 3.3 18.2 + - + +
44D LEU* 3.2 22.3 + - - +
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 3.9 21.5 - - + +
37D THR 3.0 11.2 + - - +
38D LYS* 2.8 14.4 - - + +
40D GLN* 1.3 75.6 - - - +
42D TYR* 1.3 63.0 + - + -
44D LEU* 2.8 16.7 + - + +
45D GLN* 2.9 34.0 + - - +
50D LEU* 3.9 22.9 - - + -
53D GLN 4.9 3.6 - - - +
54D GLN* 5.7 0.9 - - - -
55D VAL* 5.2 4.0 - - + -
219D ILE* 3.6 19.3 - - + +
220D PHE* 3.3 37.5 - - + -
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Residues in contact with TYR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LYS* 2.6 53.2 + - + +
39D GLU* 2.7 23.9 + - + +
41D LEU* 1.3 71.3 - - + +
43D LYS* 1.3 53.9 + - + +
45D GLN* 3.0 24.9 + - + +
46D ASP* 2.4 41.3 + - + +
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D GLU* 2.8 40.6 + - + +
40D GLN* 3.6 18.6 - - + +
42D TYR* 1.3 77.4 - - + +
44D LEU* 1.3 59.0 + - - +
46D ASP* 3.8 9.5 - - - +
47D GLY* 2.7 26.9 + - - -
49D HIS* 3.8 3.3 + - - -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D HIS* 4.0 37.9 - - + +
33D GLU* 5.1 4.9 - - - +
35D LEU* 3.9 29.2 - - + -
40D GLN 3.2 8.2 + - - +
41D LEU* 2.9 14.8 - - + +
43D LYS* 1.3 82.9 - - - +
45D GLN* 1.3 59.8 + - - +
47D GLY 3.3 0.2 + - - -
49D HIS* 2.9 59.8 + - + +
50D LEU* 3.9 23.8 - - + -
55D VAL* 4.7 1.3 - - + -
57D MET* 4.9 2.2 - - + -
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C ARG* 5.2 3.6 - - - +
41D LEU* 2.9 38.0 + - + +
42D TYR* 3.1 40.4 - - + +
44D LEU* 1.3 78.2 - - - +
46D ASP* 1.3 53.3 + - - +
48D ASN* 2.7 33.1 + - - +
50D LEU* 3.9 13.2 + - + +
53D GLN* 3.1 57.1 + - - +
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Residues in contact with ASP 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 2.4 28.3 + - + +
43D LYS* 3.8 9.6 - - - +
45D GLN* 1.3 73.9 - - - +
47D GLY* 1.3 63.7 + - - +
48D ASN* 3.0 8.7 + - - +
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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