Contacts of the helix formed by residues 140 - 155 (chain P) in PDB entry 5GJQ
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 ILE 140 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139P GLU* 1.3 75.7 - - - +
141P GLU* 1.3 60.5 + - - +
142P ARG 3.6 0.2 - - - -
143P ALA* 4.2 6.9 + - + +
144P ARG* 3.5 24.6 + - - +
176P SER* 4.1 22.4 - - - +
177P MET* 4.6 10.8 - - + -
178P GLU 5.4 1.6 - - - +
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Residues in contact with GLU 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P MET 3.3 7.6 - - - +
107P GLN* 1.6 54.5 - - - +
108P CYS* 2.7 25.2 + - + +
111P TYR* 3.7 4.7 - - - +
127P THR* 3.8 8.5 - - + +
131P VAL* 4.8 9.3 - - + +
139P GLU 3.2 2.4 - - - +
140P ILE* 1.3 79.4 - - - +
142P ARG* 1.3 66.2 + - - +
143P ALA 3.3 0.2 - - - -
144P ARG* 3.0 38.9 - - - +
145P LEU* 3.1 18.1 + - + +
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Residues in contact with ARG 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392K TYR* 5.9 1.9 - - - -
127P THR* 6.0 0.2 - - - -
128P LEU* 4.4 15.6 - - + +
131P VAL* 3.0 47.1 - - + +
132P THR* 3.1 42.3 + - - +
139P GLU* 4.0 9.3 + - - +
141P GLU* 1.3 79.1 - - - +
143P ALA* 1.3 64.1 + - - +
145P LEU* 3.1 7.6 + - - +
146P THR* 2.9 28.9 + - + +
169P LEU* 3.3 29.1 - - + +
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Residues in contact with ALA 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P GLU 4.1 8.8 + - - +
140P ILE* 4.5 7.4 - - - +
141P GLU 3.3 0.8 - - - -
142P ARG* 1.3 79.0 - - - +
144P ARG* 1.3 54.5 + - - +
146P THR* 2.2 37.9 + - - +
147P LYS* 3.0 11.9 + - - +
169P LEU* 3.6 20.1 - - + +
173P THR* 5.4 7.4 - - + +
185P PHE* 4.1 22.5 - - + -
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Residues in contact with ARG 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P CYS* 3.1 46.3 + - - +
111P TYR* 3.8 16.1 - - - +
112P VAL* 6.3 0.6 - - - +
140P ILE* 3.5 15.2 + - - +
141P GLU* 3.0 40.4 - - - +
143P ALA* 1.3 78.1 - - - +
145P LEU* 1.3 59.6 + - + +
147P LYS* 4.0 21.7 - - + +
148P THR* 3.7 17.5 + - - -
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Residues in contact with LEU 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P TYR* 4.0 30.5 - - + +
124P LEU* 4.2 18.3 - - + +
127P THR* 4.2 18.8 - - + -
128P LEU* 5.6 4.3 - - + +
141P GLU* 3.1 18.3 + - + +
142P ARG* 3.1 6.5 + - - +
144P ARG* 1.3 77.4 - - + +
146P THR* 1.3 59.7 + - - +
147P LYS 3.5 0.4 - - - -
148P THR* 4.1 6.2 - - - -
149P LEU* 2.8 36.4 + - + +
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Residues in contact with THR 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P LEU* 5.4 2.2 - - + -
142P ARG* 2.9 22.5 + - + +
143P ALA* 2.2 39.9 + - - -
145P LEU* 1.3 72.5 - - - +
147P LYS* 1.3 65.8 + - - +
149P LEU* 3.4 19.5 - - + -
150P ALA* 2.9 26.5 + - - +
165P ILE* 4.4 10.1 - - + -
166P LEU* 4.9 6.0 - - - +
169P LEU* 3.1 39.0 - - + +
185P PHE* 5.1 4.9 - - - -
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Residues in contact with LYS 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P ALA 3.0 12.4 + - - +
144P ARG* 4.0 22.1 - - + +
146P THR* 1.3 79.5 + - - +
148P THR* 1.3 64.9 + - - +
150P ALA* 4.1 0.8 - - - +
151P THR* 3.0 27.6 + - - -
166P LEU* 5.6 3.5 - - - +
181P GLU* 3.8 28.3 - - - +
184P GLU* 4.2 12.3 - - - +
185P PHE* 3.7 45.5 - - + -
188P GLU* 5.9 3.4 - - + -
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Residues in contact with THR 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P LEU* 6.3 0.9 - - - -
144P ARG 3.7 14.4 + - - -
145P LEU* 4.1 6.5 - - - -
146P THR 3.4 0.4 - - - -
147P LYS* 1.3 79.0 - - - +
149P LEU* 1.3 64.8 + - - +
151P THR* 5.3 0.2 - - - -
152P ILE* 2.8 47.1 + - - +
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Residues in contact with LEU 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P LEU* 4.1 21.5 - - + -
128P LEU* 4.9 15.5 - - + -
145P LEU 2.8 28.0 + - - +
146P THR* 3.4 22.4 - - + -
148P THR* 1.3 73.1 - - - +
150P ALA* 1.3 63.9 + - - +
153P LYS* 2.7 61.5 + - + +
165P ILE* 2.6 35.0 - - + -
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Residues in contact with ALA 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P THR 2.9 20.0 + - - +
147P LYS 4.1 0.2 - - - +
149P LEU* 1.3 80.5 - - - +
151P THR* 1.3 62.5 + - - +
154P GLU* 3.1 6.9 - - - +
159P VAL* 5.6 0.5 - - - +
162P ALA* 2.7 35.5 - - + +
165P ILE* 3.2 23.8 - - + -
166P LEU* 3.3 29.4 - - + -
192P LEU* 5.8 0.9 - - - -
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Residues in contact with THR 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147P LYS* 3.0 16.5 + - - -
148P THR 4.7 0.2 - - - -
150P ALA* 1.3 77.0 - - - +
152P ILE* 1.3 66.2 + - - +
154P GLU* 5.2 0.2 - - - -
155P GLN* 2.8 38.9 + - - +
159P VAL* 6.1 2.5 - - - -
166P LEU* 5.0 1.1 - - - +
188P GLU* 5.0 10.7 + - - -
192P LEU* 5.5 13.7 - - - +
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Residues in contact with ILE 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P THR* 2.8 36.8 + - - +
151P THR* 1.3 83.0 - - - +
153P LYS* 1.3 67.4 + - - +
154P GLU 3.2 4.5 + - - -
155P GLN* 4.2 10.2 - - + +
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Residues in contact with LYS 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P LYS* 5.8 9.0 - - + -
149P LEU* 2.7 49.7 + - + +
150P ALA 3.4 5.2 - - - +
152P ILE* 1.3 79.9 - - - +
154P GLU* 1.3 63.6 + - + +
158P ASP* 5.7 2.8 - - - -
161P GLU* 3.9 9.3 + - - +
162P ALA* 2.8 40.8 - - + +
165P ILE* 3.9 10.7 - - - +
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Residues in contact with GLU 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150P ALA 3.1 5.8 - - - +
153P LYS* 1.3 78.6 - - + +
155P GLN* 1.3 72.4 + - - +
156P ASN* 2.7 24.4 + - - +
158P ASP* 3.1 48.9 - - + +
159P VAL* 3.9 8.3 - - + +
162P ALA* 2.7 40.6 - - + -
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Residues in contact with GLN 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P THR* 2.8 30.0 + - - +
152P ILE* 4.2 11.9 - - + +
154P GLU* 1.3 87.2 - - - +
156P ASN* 1.3 68.8 + - - +
159P VAL* 5.1 6.7 - - - +
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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