Contacts of the helix formed by residues 118 - 131 (chain F) in PDB entry 6D6Q
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 GLU 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107E ASN* 5.1 0.9 + - - -
111E ARG* 3.9 9.1 + - - -
102F ARG* 4.8 10.1 - - - +
111F ARG* 6.2 2.7 - - - +
117F CYS* 1.3 77.5 - - + +
119F GLU* 1.3 72.4 + - - +
120F ARG 3.2 1.6 - - - -
121F GLU* 2.7 32.8 + - - +
122F LEU* 3.0 55.8 + - + +
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Residues in contact with GLU 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F PHE* 4.0 34.0 - - + +
101F ARG* 4.7 11.7 - - + -
102F ARG* 4.4 16.8 + - + +
111F ARG* 3.5 31.3 + - - -
113F PRO 5.1 3.1 - - - +
114F PRO 4.8 5.6 - - - +
115F GLY* 3.4 17.9 - - - -
116F GLY 3.1 22.3 + - - +
117F CYS* 3.6 0.7 + - - +
118F GLU* 1.3 86.6 + - - +
120F ARG* 1.3 60.4 + - + +
122F LEU* 3.3 2.6 + - - +
123F ALA* 2.9 27.8 + - - +
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Residues in contact with ARG 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ASP* 5.6 7.1 - - - +
103E THR* 4.5 29.1 + - + -
115F GLY 5.5 0.8 + - - -
116F GLY* 4.0 35.5 + - - -
117F CYS 4.6 3.6 - - - +
118F GLU* 3.2 0.8 - - - +
119F GLU* 1.3 76.7 + - + +
121F GLU* 1.3 60.7 + - - +
123F ALA* 3.2 7.6 + - - +
124F LEU* 2.9 42.5 + - + +
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Residues in contact with GLU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ASN* 3.7 36.0 + - + +
108E THR* 5.2 1.4 + - - +
111E ARG* 2.7 41.8 + - - +
240E ARG* 5.3 12.8 + - - +
117F CYS 4.2 6.7 + - - +
118F GLU* 2.7 39.1 + - - +
120F ARG* 1.3 78.7 - - - +
122F LEU* 1.3 59.9 + - + +
124F LEU* 3.2 10.4 + - - +
125F ALA* 3.0 25.0 + - - +
226F LEU* 4.6 7.8 - - + +
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ARG* 5.5 0.2 - - - +
100F PHE* 3.6 32.8 - - + -
102F ARG* 3.9 17.0 - - - +
118F GLU* 3.0 37.6 + - + +
119F GLU 3.9 2.9 - - - +
121F GLU* 1.3 76.7 - - + +
123F ALA* 1.3 57.4 + - - +
125F ALA* 3.2 5.4 + - + +
126F LEU* 2.9 33.1 + - - +
157F ALA* 6.1 2.2 - - + -
158F LEU* 3.6 39.1 - - + +
226F LEU* 4.6 16.2 - - + -
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Residues in contact with ALA 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F CYS* 2.9 48.2 - - - +
99F ASP* 5.1 0.4 - - - -
100F PHE* 4.2 17.0 - - - +
119F GLU 2.9 17.2 + - - +
120F ARG* 3.4 10.8 - - - +
121F GLU 3.2 0.2 - - - -
122F LEU* 1.3 73.6 - - - +
124F LEU* 1.3 69.1 + - + +
126F LEU* 3.1 2.5 + - - +
127F GLN* 2.9 8.4 + - - +
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ASP* 4.3 23.3 - - - +
104E GLU* 4.8 19.3 - - + +
240E ARG* 4.4 15.5 - - - +
120F ARG* 2.9 34.1 + - + +
121F GLU* 3.4 11.7 - - + +
123F ALA* 1.3 77.8 - - + +
125F ALA* 1.3 62.8 + - - +
127F GLN* 3.3 19.4 + - - +
128F GLU* 2.9 42.0 + - + +
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Residues in contact with ALA 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E ARG* 5.4 0.8 - - - +
121F GLU 3.0 13.1 + - - +
122F LEU* 3.3 14.1 - - - +
123F ALA 3.1 0.2 - - - -
124F LEU* 1.3 77.4 - - - +
126F LEU* 1.3 63.9 + - - +
128F GLU* 3.3 11.6 + - - +
129F ALA* 2.9 25.3 + - - +
158F LEU* 4.2 21.1 - - + -
162F LEU* 4.7 1.6 - - - -
224F GLY* 5.4 1.2 - - - -
225F LEU 6.2 0.4 - - - +
226F LEU* 4.9 14.6 - - + -
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F CYS* 3.9 20.2 - - + -
99F ASP 5.4 0.2 - - - -
100F PHE* 4.0 33.4 - - + +
122F LEU 2.9 16.4 + - - +
123F ALA 3.1 4.9 + - - +
125F ALA* 1.3 76.0 - - - +
127F GLN* 1.3 58.5 + - - +
129F ALA 3.2 1.2 + - - -
130F LEU* 2.9 41.7 + - + +
146F VAL* 5.8 1.8 - - + -
148F ALA* 4.5 12.1 - - + -
158F LEU* 3.9 7.9 - - + -
161F ALA* 3.9 12.6 - - + +
162F LEU* 3.3 44.9 - - + +
165F ALA* 5.3 7.0 - - + -
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Residues in contact with GLN 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ARG* 6.0 1.8 - - - +
96F LEU* 3.9 25.4 + - + +
97F LEU* 5.4 3.3 - - - +
98F CYS* 3.7 14.6 + - - -
123F ALA 2.9 14.3 + - - +
124F LEU* 3.7 22.0 - - - +
126F LEU* 1.3 76.8 - - - +
128F GLU* 1.3 60.1 + - + +
130F LEU* 4.6 3.6 - - - +
131F GLU* 3.0 65.4 + - + +
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E GLU* 4.4 1.0 - - - +
240E ARG* 3.2 26.4 + - - -
241E LYS* 2.9 26.6 - - - +
242E VAL* 3.3 20.8 - - - +
243E GLY 3.6 26.2 - - - +
124F LEU* 2.9 32.6 + - + +
125F ALA* 3.7 9.2 - - - +
127F GLN* 1.3 78.4 - - + +
129F ALA* 1.3 57.4 + - - +
130F LEU 3.5 0.2 - - - -
131F GLU* 4.8 4.9 - - - +
132F PRO* 3.3 14.8 - - - +
223F ALA 3.0 16.5 - - - +
224F GLY* 4.9 3.8 - - - -
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ALA 2.9 16.9 + - - +
128F GLU* 1.3 78.8 - - - +
130F LEU* 1.3 60.2 + - - +
132F PRO* 3.6 3.9 - - - +
133F ALA 4.7 1.2 + - - -
162F LEU* 3.4 31.2 - - + -
180F VAL* 3.9 14.7 - - + +
214F ALA* 4.7 2.0 - - + -
223F ALA* 3.4 26.2 - - + +
224F GLY* 4.0 18.8 - - - +
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Residues in contact with LEU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F LEU* 3.8 23.8 - - + -
98F CYS* 5.4 2.9 - - + -
126F LEU* 2.9 30.5 + - + +
127F GLN* 4.2 1.3 - - - +
129F ALA* 1.3 78.5 - - - +
131F GLU* 1.3 66.6 + - - +
132F PRO* 3.0 4.3 - - - -
133F ALA* 3.1 14.0 + - + +
134F VAL* 3.1 19.2 + - + +
146F VAL* 4.9 9.2 - - + -
162F LEU* 4.5 10.8 - - + +
165F ALA* 3.9 21.1 - - + -
166F ALA* 4.5 18.2 - - - +
169F LEU* 4.5 13.5 - - + -
180F VAL* 4.2 22.2 - - + -
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Residues in contact with GLU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E LYS* 2.7 49.7 - - + +
93F ARG* 5.2 5.9 + - - -
96F LEU* 3.4 27.0 - - + +
127F GLN* 3.0 49.9 + - + +
128F GLU* 4.8 2.3 - - - +
130F LEU* 1.3 73.6 - - - +
132F PRO* 1.3 63.5 - - + +
134F VAL* 2.9 22.6 - - - +
136F LEU* 4.9 12.9 - - + +
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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