Contacts of the helix formed by residues 68 - 78 (chain D) 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 THR 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D ARG* 3.7 25.8 - - + +
18D SER* 5.0 4.0 - - - +
19D VAL* 4.6 7.9 - - + -
56D PRO* 3.4 15.1 - - + +
67D GLN* 1.3 72.5 - - - +
69D ARG* 1.3 71.2 + - + +
71D ILE* 3.2 12.3 + - - +
72D LEU* 3.0 43.0 + - + +
100D LEU* 5.6 5.2 - - + -
301D IBG 2.9 30.2 + - - -
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Residues in contact with ARG 69 (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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69C ARG* 3.4 22.5 - - - +
97C GLU* 3.4 28.8 + - + -
15D ARG* 6.0 1.8 - - - +
67D GLN* 3.2 1.8 + - - +
68D THR* 1.3 79.5 - - - +
70D SER* 1.3 59.0 + - - +
72D LEU* 3.4 7.8 + - - +
73D HIS* 2.9 50.2 + - + +
97D GLU* 2.7 32.8 + - - +
100D LEU* 3.8 38.6 - - + +
101D ASP* 4.6 10.7 + - - -
301D IBG 4.6 17.2 + - - -
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Residues in contact with SER 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C THR* 5.1 4.5 - - - +
93C ASP* 2.9 39.7 + - - +
94C MET* 3.7 15.5 - - - -
97C GLU* 3.1 18.5 - - - +
65D LEU* 5.5 2.0 - - - -
66D VAL 3.7 11.4 - - - -
67D GLN* 2.9 11.7 + - - +
69D ARG* 1.3 73.5 - - - +
71D ILE* 1.3 67.1 + - - +
73D HIS* 3.4 2.9 + - - +
74D TYR* 3.0 23.2 + - - +
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Residues in contact with ILE 71 (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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19D VAL* 4.4 17.7 - - + -
56D PRO* 3.9 37.7 - - + +
58D VAL* 4.1 19.5 - - + -
60D ILE* 6.3 0.4 - - + -
65D LEU* 3.8 36.3 - - + +
66D VAL 3.9 3.1 - - - +
67D GLN 2.9 20.5 + - - +
68D THR* 3.4 8.5 - - - +
70D SER* 1.3 79.4 - - - +
72D LEU* 1.3 62.3 + - - +
74D TYR* 3.0 15.2 + - - +
75D ILE* 3.1 32.2 + - + +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D SER* 4.0 17.3 - - - -
19D VAL* 3.9 30.7 - - + +
22D VAL* 3.8 28.3 - - + +
68D THR* 3.0 28.8 + - + +
69D ARG* 3.7 10.3 - - - +
70D SER 3.3 0.2 - - - -
71D ILE* 1.3 76.0 - - - +
73D HIS* 1.3 65.6 + - + +
75D ILE* 3.3 5.5 + - + +
76D ALA* 3.0 23.2 + - - +
96D VAL* 5.4 3.1 - - + -
100D LEU* 4.8 14.1 - - + -
155D LEU* 4.2 18.4 - - + +
159D ILE* 4.3 12.6 - - + -
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Residues in contact with HIS 73 (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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73C HIS* 3.9 25.6 - + - -
93C ASP* 2.7 29.7 + - - +
97C GLU* 5.0 0.7 - - - -
69D ARG* 2.9 28.9 + - + +
70D SER 3.6 5.2 - - - +
72D LEU* 1.3 80.1 - - + +
74D TYR* 1.3 63.4 + - - +
76D ALA* 3.7 1.8 - - - +
77D ASP* 2.9 31.2 + - - +
82D PHE* 3.6 35.2 - + + -
89D ARG* 5.3 1.8 - - - +
93D ASP* 4.6 5.7 + - - -
96D VAL* 5.8 3.8 - - + +
97D GLU* 4.2 12.3 + - - -
155D LEU* 4.5 8.7 - - + -
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Residues in contact with TYR 74 (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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86C LEU* 3.9 13.7 - - + -
87C LYS* 3.1 32.1 + - - -
90C THR* 3.7 25.6 - - + -
60D ILE* 3.8 29.4 - - + -
61D ASP* 2.5 36.6 + - + +
63D MET* 4.5 9.4 - - + -
65D LEU* 3.7 23.6 - - + -
70D SER 3.0 14.2 + - - +
71D ILE 3.0 7.6 + - - +
73D HIS* 1.3 79.4 - - - +
75D ILE* 1.3 68.0 - - + +
77D ASP* 3.1 3.8 + - - +
78D LYS* 2.8 50.5 + - + +
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Residues in contact with ILE 75 (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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19D VAL* 4.1 11.0 - - + +
22D VAL* 3.8 25.1 - - + +
23D LEU* 4.0 38.1 - - + +
26D ALA* 5.0 2.0 - - + -
58D VAL* 5.6 2.2 - - + -
60D ILE* 4.4 20.4 - - + -
71D ILE* 3.1 31.5 + - + +
72D LEU* 3.8 7.9 - - + +
74D TYR* 1.3 80.8 - - + +
76D ALA* 1.3 65.1 + - - +
78D LYS* 3.0 4.0 + - - -
79D HIS* 2.9 44.8 + - + +
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Residues in contact with ALA 76 (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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22D VAL* 5.0 0.6 - - - +
72D LEU 3.0 17.7 + - - +
73D HIS 3.7 3.6 - - - +
75D ILE* 1.3 77.4 - - - +
77D ASP* 1.3 58.9 + - - +
79D HIS 2.9 15.1 + - - -
80D ASN* 3.2 1.7 + - - -
81D LEU* 3.0 47.3 + - + -
82D PHE* 3.7 20.0 + - + -
155D LEU* 4.0 15.9 - - + -
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Residues in contact with ASP 77 (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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86C LEU* 4.0 29.3 - - + +
89C ARG* 4.5 3.8 + - - -
73D HIS* 2.9 19.0 + - - +
74D TYR 3.6 4.0 - - - +
76D ALA* 1.3 79.4 - - - +
78D LYS* 1.3 62.9 + - - +
79D HIS 3.4 0.3 + - - -
80D ASN 4.3 3.5 + - - +
82D PHE* 3.4 11.1 - - - +
89D ARG* 2.7 47.3 + - - -
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Residues in contact with LYS 78 (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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86C LEU* 3.6 27.9 - - + +
87C LYS* 4.7 5.8 - - - +
60D ILE* 5.9 0.7 - - + -
61D ASP* 4.1 7.4 - - - +
74D TYR* 2.8 53.2 + - + +
75D ILE* 3.0 3.3 + - - +
77D ASP* 1.3 78.7 - - - +
79D HIS* 1.3 85.1 + - + +
80D ASN 3.8 0.9 - - - -
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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