Contacts of the helix formed by residues 114 - 126 (chain D) in PDB entry 1EGE
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 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D ASN* 4.0 14.7 + - - -
113D ASN* 1.2 74.2 - - - +
115D GLN* 1.3 64.2 + - - +
117D LYS* 3.2 10.2 + - - +
118D LYS* 2.8 66.9 + - - +
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Residues in contact with GLN 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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113D ASN* 2.9 16.7 + - - +
114D ASP* 1.3 72.8 - - - +
116D GLN* 1.3 69.8 + - + +
118D LYS* 3.0 17.2 + - - +
119D LYS* 3.0 53.2 + - - +
120D TYR* 6.0 0.2 - - - -
235D GLU* 5.4 16.4 - - + +
236D ASN* 5.7 3.1 - - - +
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Residues in contact with GLN 116 (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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108D ILE* 4.6 8.8 - - + +
111D ALA 3.8 0.2 - - - +
112D GLY* 3.3 9.8 - - - -
113D ASN* 2.8 50.6 + - - +
115D GLN* 1.3 76.2 - - + +
117D LYS* 1.3 62.6 + - - +
120D TYR* 3.2 42.2 + - + +
198D ILE* 5.4 3.4 - - + -
235D GLU 3.2 22.6 + - - +
236D ASN* 3.6 15.9 + - - +
237D VAL 3.0 27.5 + - - -
238D LEU* 3.2 23.4 + - + +
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Residues in contact with LYS 117 (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 PRO* 4.7 18.3 - - - +
69D ASN* 5.6 4.5 - - - +
70D CYS* 3.9 14.9 - - - -
108D ILE* 3.9 20.0 - - + +
109D ILE* 4.3 19.1 + - - +
112D GLY* 3.0 36.9 + - - +
113D ASN 2.7 27.4 + - - +
114D ASP* 3.7 7.9 - - - +
116D GLN* 1.3 75.2 - - - +
118D LYS* 1.3 56.0 + - - +
121D LEU* 2.8 41.9 + - + +
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Residues in contact with LYS 118 (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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69D ASN* 5.0 2.5 - - - +
70D CYS* 4.2 17.7 - - - +
114D ASP* 2.8 78.3 + - - +
115D GLN* 3.0 19.3 + - - +
117D LYS* 1.3 68.7 - - - +
119D LYS* 1.3 63.4 + - - +
120D TYR 3.1 5.4 + - - -
122D GLY* 3.1 20.4 + - - +
123D ARG* 3.1 14.7 + - - +
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Residues in contact with LYS 119 (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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115D GLN* 3.0 43.3 + - - +
116D GLN 4.4 1.3 - - - +
118D LYS* 1.3 76.7 - - - +
120D TYR* 1.3 92.9 + - + +
123D ARG* 2.9 39.2 + - - +
200D GLU* 3.1 26.2 + - - -
236D ASN* 5.5 2.7 - - - +
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Residues in contact with TYR 120 (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 ILE* 5.3 1.8 - - + -
115D GLN* 6.0 0.2 - - - -
116D GLN* 3.2 29.7 + - + +
118D LYS 3.1 0.4 - - - -
119D LYS* 1.3 116.7 + - + +
121D LEU* 1.3 72.6 + - + +
122D GLY 3.4 0.4 - - - -
123D ARG* 3.5 13.0 + - + +
124D MET* 3.6 4.3 - - - +
175D TRP* 3.4 39.5 + + + +
198D ILE* 3.7 40.6 + - + +
200D GLU* 3.4 28.5 + - + +
236D ASN* 2.7 41.8 + - - -
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Residues in contact with LEU 121 (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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66D ILE* 3.9 28.7 - - + +
67D PRO* 3.7 30.7 - - + -
70D CYS* 4.6 3.8 - - + -
105D GLN* 5.0 3.8 - - + +
108D ILE* 3.5 32.5 - - + -
109D ILE* 3.8 19.3 - - + -
117D LYS* 2.8 35.6 + - + +
120D TYR* 1.3 77.0 - - + +
122D GLY* 1.3 55.0 + - - +
123D ARG 2.8 8.0 + - - -
124D MET* 2.8 22.7 + - - +
125D THR* 3.1 10.9 + - - -
175D TRP* 4.7 11.7 - - + -
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Residues in contact with GLY 122 (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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70D CYS* 4.1 10.8 + - - +
117D LYS 3.6 1.0 + - - -
118D LYS* 3.1 18.9 + - - +
121D LEU* 1.3 77.8 - - - +
123D ARG* 1.3 60.9 + - - +
125D THR* 3.0 30.2 - - - -
126D GLU* 3.1 18.2 + - - +
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Residues in contact with ARG 123 (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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118D LYS* 3.1 16.6 + - - +
119D LYS* 2.9 56.7 + - - +
120D TYR* 3.5 13.7 - - + +
121D LEU 2.8 2.4 + - - -
122D GLY* 1.3 69.6 - - - +
124D MET* 1.3 61.5 + - + +
125D THR 3.0 4.3 - - - -
126D GLU* 3.0 19.0 + - - +
127D GLU* 2.9 29.7 + - - +
129D LEU* 4.8 16.0 - - + +
174D ASN* 5.1 5.8 - - - +
175D TRP* 5.6 2.2 - - + +
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Residues in contact with MET 124 (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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57D TRP* 3.7 11.3 + - - -
63D ASN* 3.4 27.0 + - - +
66D ILE* 4.2 3.8 - - + -
101D ASN* 3.2 28.3 - - - +
105D GLN* 3.3 23.6 - - - +
120D TYR 3.6 9.6 - - - +
121D LEU* 3.3 13.9 - - - +
123D ARG* 1.3 77.2 - - - +
125D THR* 1.3 61.1 + - - +
127D GLU 2.9 20.3 - - - +
128D PRO* 4.8 0.3 - - - +
129D LEU* 3.1 30.1 - - - +
130D MET 3.8 2.7 - - - +
131D CYS* 3.4 20.6 - - + -
174D ASN* 5.0 0.7 - - - -
175D TRP* 3.6 18.4 - - + +
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Residues in contact with THR 125 (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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57D TRP* 4.2 10.6 + - - -
66D ILE* 4.4 9.6 - - - +
70D CYS 3.2 20.6 + - - +
71D GLY* 3.7 23.1 - - - +
72D GLY* 4.2 2.4 - - - +
121D LEU 3.1 6.5 + - - -
122D GLY* 3.0 31.6 - - - -
124D MET* 1.3 81.4 - - - +
126D GLU* 1.3 59.9 + - + +
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Residues in contact with GLU 126 (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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57D TRP* 3.7 13.2 - - - -
122D GLY 3.2 15.7 - - - +
123D ARG* 3.0 20.1 + - - +
125D THR* 1.3 82.2 - - + +
127D GLU* 1.3 61.0 + - + +
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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