Contacts of the helix formed by residues 106 - 116 (chain D) in PDB entry 5EGU
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 ASP 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D PHE* 3.7 6.5 - - - +
85D GLN* 3.1 30.9 - - - +
86D PRO* 3.2 25.0 - - + +
87D VAL* 5.3 1.1 - - + +
105D MET* 1.3 82.6 + - - +
107D MET* 1.3 58.8 + - - +
108D GLY 3.0 9.7 + - - -
109D THR* 2.5 42.0 + - - -
110D ILE* 3.0 32.8 + - - +
132D MET* 3.8 9.2 - - - -
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Residues in contact with MET 107 (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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71D LEU* 3.6 13.1 - - + +
74D LEU* 3.8 43.7 - - + +
75D TRP* 3.7 17.9 - - + -
80D ALA* 4.0 30.3 - - + +
83D PHE* 2.7 32.6 + - + +
84D GLN* 4.3 5.2 - - + -
106D ASP* 1.3 68.7 - - - +
108D GLY* 1.3 58.2 + - - +
109D THR 3.3 0.2 - - - -
110D ILE* 3.7 7.0 - - + -
111D LYS* 2.9 29.6 + - - +
129D PHE* 4.1 11.9 - - + -
132D MET* 3.6 21.8 - - + -
153D LEU* 5.1 3.6 - - + -
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Residues in contact with GLY 108 (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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75D TRP* 3.6 11.8 - - - -
84D GLN 3.4 19.1 + - - -
85D GLN* 4.8 0.9 - - - -
86D PRO* 5.6 1.3 - - - -
106D ASP* 3.0 9.7 + - - -
107D MET* 1.3 74.9 - - - +
109D THR* 1.3 63.3 + - - +
111D LYS* 3.3 4.5 + - - +
112D LYS* 3.0 24.6 + - - +
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Residues in contact with THR 109 (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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86D PRO* 4.0 11.7 - - - +
105D MET* 3.8 15.9 - - + -
106D ASP* 2.5 33.5 + - - -
108D GLY* 1.3 72.3 - - - +
110D ILE* 1.3 66.2 + - - +
112D LYS* 3.4 7.7 + - + +
113D ARG* 2.9 53.3 + - + +
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Residues in contact with ILE 110 (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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71D LEU* 4.3 3.4 - - + -
105D MET* 3.9 6.3 - - + -
106D ASP 3.0 29.0 + - - +
107D MET* 3.7 9.6 - - + +
108D GLY 3.3 0.2 - - - -
109D THR* 1.3 76.1 - - - +
111D LYS* 1.3 52.4 + - - +
113D ARG* 3.2 2.6 + - - +
114D LEU* 2.8 52.2 + - + +
119D TYR* 3.7 15.2 - - - +
125D CYS* 4.0 3.1 - - - -
128D ASP* 3.8 24.0 - - + +
129D PHE* 3.9 59.5 - - + +
132D MET* 4.7 2.7 - - - -
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Residues in contact with LYS 111 (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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67D LEU* 4.7 2.9 - - + -
71D LEU* 3.6 32.5 - - + -
75D TRP* 4.3 29.3 - - + +
107D MET 2.9 18.6 + - - +
108D GLY* 3.7 5.2 - - - +
109D THR 3.2 0.4 - - - -
110D ILE* 1.3 74.2 - - - +
112D LYS* 1.3 67.2 + - - +
114D LEU* 3.2 6.5 + - - +
115D GLU* 2.9 59.1 + - + +
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Residues in contact with LYS 112 (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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108D GLY 3.0 17.9 + - - +
109D THR* 3.7 7.4 - - - +
111D LYS* 1.3 76.7 - - - +
113D ARG* 1.3 66.1 + - + +
115D GLU* 3.2 13.0 + - - +
116D ASN* 3.0 44.2 + - + +
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Residues in contact with ARG 113 (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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64B GLN* 5.6 2.6 - - - +
105D MET* 3.3 24.2 - - - +
109D THR* 2.9 39.9 + - + +
110D ILE* 3.5 3.8 - - - +
112D LYS* 1.3 76.3 - - + +
114D LEU* 1.3 63.2 + - - +
116D ASN* 3.3 1.2 + - - -
117D ASN 3.3 2.4 + - - -
118D TYR* 3.0 89.6 + - + -
119D TYR* 3.4 24.2 - - + -
128D ASP* 2.7 31.1 + - - -
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Residues in contact with LEU 114 (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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59D GLN* 3.0 33.3 + - - +
63D LEU* 3.6 47.3 - - + +
66D LEU* 4.1 7.2 - - + +
67D LEU* 3.8 40.9 - - + +
71D LEU* 4.6 4.0 - - + -
110D ILE* 2.8 40.2 + - + +
111D LYS* 3.5 6.1 - - - +
113D ARG* 1.3 74.5 - - - +
115D GLU* 1.3 60.7 + - - +
116D ASN 3.6 0.3 + - - -
117D ASN 3.7 2.1 + - - -
119D TYR* 3.9 12.8 - - + -
125D CYS* 4.1 9.2 - - - -
129D PHE* 5.4 0.2 - - + -
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Residues in contact with GLU 115 (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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67D LEU* 4.4 20.9 - - + +
111D LYS* 2.9 55.9 + - - +
112D LYS* 3.2 12.3 + - - +
114D LEU* 1.3 75.4 - - - +
116D ASN* 1.3 69.1 + - - +
117D ASN 3.4 2.1 + - - -
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Residues in contact with ASN 116 (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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112D LYS* 3.0 46.3 + - + +
113D ARG* 4.4 2.2 - - - +
114D LEU 3.3 0.2 - - - -
115D GLU* 1.3 86.6 + - - +
117D ASN* 1.3 69.1 + - - +
118D TYR* 3.0 5.9 + - + +
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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