Contacts of the helix formed by residues 38 - 46 (chain H) in PDB entry 1GUL
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H THR* 1.4 72.1 - - - +
39H GLU* 1.3 52.9 + - - +
41H LEU* 2.8 10.3 + - + +
42H TYR* 2.6 64.8 + - + +
217H TYR 4.3 1.8 + - - -
218H ASN 3.1 23.8 + - - +
219H ILE* 3.4 27.2 - - - +
220H PHE* 2.6 31.7 + - - +
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Residues in contact with GLU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H THR* 3.1 10.1 + - - +
38H LYS* 1.3 82.1 - - - +
40H GLN* 1.3 66.5 + - - +
42H TYR* 3.0 16.1 + - + +
43H LYS* 2.9 54.9 + - + +
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Residues in contact with GLN 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H PHE 4.0 13.1 + - - -
35H LEU* 3.9 14.3 - - + +
36H GLU* 2.5 43.5 + - - +
37H THR* 2.6 30.5 + - + +
39H GLU* 1.3 77.8 - - - +
41H LEU* 1.3 62.2 + - - +
43H LYS* 3.3 15.6 + - + +
44H LEU* 3.1 21.8 + - - +
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Residues in contact with LEU 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H LEU* 3.9 21.7 - - + +
37H THR 3.2 10.1 + - - +
38H LYS* 2.8 13.8 + - + +
40H GLN* 1.3 77.7 - - - +
42H TYR* 1.3 65.6 + - + +
44H LEU* 2.8 16.0 + - + +
45H GLN* 2.9 35.0 + - - +
50H LEU* 3.9 18.8 - - + -
53H GLN 4.6 2.5 - - - +
55H VAL* 5.1 3.4 - - + -
219H ILE* 3.4 29.4 - - + +
220H PHE* 3.6 26.7 - - + -
301H IBG 4.1 13.9 - - - +
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Residues in contact with TYR 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F SER 4.0 7.7 + - - -
177F ALA* 6.3 0.4 - - - -
179F PRO* 3.5 39.2 - - + +
182F GLN* 3.8 24.9 + - - -
38H LYS* 2.6 48.3 + - + +
39H GLU* 3.0 19.0 + - + +
41H LEU* 1.3 75.6 - - + +
43H LYS* 1.3 55.7 + - + +
45H GLN* 3.0 21.3 - - + +
46H ASP* 2.5 40.6 + - + +
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Residues in contact with LYS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLU* 2.9 43.6 + - + +
40H GLN* 3.9 15.0 - - + +
41H LEU 3.2 0.2 - - - -
42H TYR* 1.3 79.0 - - + +
44H LEU* 1.3 62.5 + - - +
46H ASP* 3.8 8.0 - - - +
47H GLY* 2.9 20.3 + - - -
49H HIS* 4.0 2.9 + - - -
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H HIS* 4.0 41.5 - - + +
33H GLU* 5.1 5.6 - - - +
35H LEU* 3.8 31.4 - - + -
40H GLN 3.1 8.2 + - - +
41H LEU* 3.0 10.8 - - - +
43H LYS* 1.3 79.0 - - - +
45H GLN* 1.3 62.9 + - - +
47H GLY 3.5 0.2 + - - -
49H HIS* 2.9 55.3 + - + +
50H LEU* 4.0 27.3 + - + -
55H VAL* 4.6 0.9 - - + -
57H MET* 4.9 1.3 - - + -
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Residues in contact with GLN 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G ARG* 4.5 3.8 - - - +
41H LEU* 2.9 23.6 + - - +
42H TYR* 3.0 37.0 - - + +
44H LEU* 1.3 79.2 - - - +
46H ASP* 1.3 55.9 + - - +
48H ASN* 2.8 31.5 + - - +
50H LEU* 3.7 18.2 - - + -
53H GLN* 3.0 57.1 + - - +
301H IBG 3.3 18.4 + - - -
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Residues in contact with ASP 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ARG* 3.0 42.7 + - - -
42H TYR* 2.5 24.8 + - + +
43H LYS* 3.8 6.9 - - - +
45H GLN* 1.3 74.1 - - - +
47H GLY* 1.3 60.3 + - - +
48H ASN* 3.0 15.6 + - - +
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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