Contacts of the helix formed by residues 139 - 157 (chain P) in PDB entry 5LN3
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 139 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98P LYS* 4.0 9.9 - - - +
99P GLN* 3.2 37.5 + - - +
102P ALA* 3.8 14.8 - - - +
136P ILE* 3.4 40.6 - - + +
137P TYR* 3.1 7.0 - - - +
138P VAL* 1.4 76.5 - - + +
140P ILE* 1.4 63.0 + - - +
141P GLU* 3.4 3.4 + - - +
142P ARG* 3.0 47.6 + - + +
143P ALA* 3.7 16.1 + - - +
173P THR* 5.4 1.4 - - - +
174P TYR* 4.7 0.9 - - - -
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Residues in contact with ILE 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P GLN* 5.9 0.4 - - - +
138P VAL 4.0 0.4 + - - -
139P GLU* 1.4 69.2 - - - +
141P GLU* 1.4 70.9 + - + +
142P ARG 3.4 0.2 - - - -
143P ALA* 3.2 8.4 + - - +
144P ARG* 3.0 45.8 + - + +
174P TYR* 3.6 21.1 - - + +
178P GLU* 3.7 9.9 - - - +
181P GLU* 3.3 33.7 - - - +
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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
----------------------------------------------------------
99P GLN* 3.5 26.0 + - - +
102P ALA* 4.0 17.0 - - + +
103P LYS* 3.5 46.6 + - - +
106P GLN* 3.5 19.8 + - + +
139P GLU* 3.4 2.7 - - + +
140P ILE* 1.4 83.0 - - + +
142P ARG* 1.4 64.5 + - + +
144P ARG* 3.3 24.1 + - - +
145P LEU* 3.3 21.7 + - + +
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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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98P LYS* 4.0 25.9 + - - +
102P ALA* 4.7 8.1 - - + +
130P MET* 3.6 53.7 - - - +
131P VAL* 4.1 1.4 - - - +
134P GLY* 3.6 5.5 - - - -
135P LYS* 3.2 24.0 - - - +
136P ILE 3.0 23.6 + - - +
137P TYR* 3.6 26.9 - - + -
139P GLU* 3.0 42.5 + - + +
141P GLU* 1.4 73.5 - - - +
143P ALA* 1.4 63.2 + - - +
145P LEU* 3.2 13.0 + - - +
146P THR* 3.1 26.1 + - - -
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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
----------------------------------------------------------
137P TYR* 4.3 2.9 - - + -
139P GLU 3.7 8.9 + - - +
140P ILE* 3.2 13.5 + - - +
142P ARG* 1.4 77.2 - - - +
144P ARG* 1.4 64.6 + - + +
146P THR* 3.3 4.2 + - - -
147P LYS* 3.1 20.1 + - - +
169P LEU* 4.1 17.0 - - + +
173P THR* 3.6 28.9 - - + -
174P TYR* 6.3 0.9 - - + -
181P GLU* 5.6 4.5 - - - +
185P PHE* 5.1 10.3 - - + -
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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
----------------------------------------------------------
106P GLN* 3.9 34.2 - - - +
140P ILE* 3.0 30.4 + - + +
141P GLU* 3.8 17.9 + - - +
142P ARG 3.2 0.4 - - - -
143P ALA* 1.4 76.9 - - + +
145P LEU* 1.3 57.4 + - - +
147P LYS* 3.0 23.3 + - + +
148P THR* 2.9 20.6 + - - +
181P GLU* 6.4 2.7 - - - -
185P PHE* 6.5 0.2 - - - -
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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
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102P ALA 5.0 1.1 - - - +
105P VAL* 4.5 10.5 - - + -
106P GLN* 3.4 44.0 - - + +
109P CYS* 3.6 38.1 - - + -
125P ILE* 5.2 5.7 - - + +
128P LEU* 6.0 4.0 - - + -
130P MET 6.0 0.7 - - - +
131P VAL* 3.6 19.0 - - + +
141P GLU 3.4 17.0 - - - +
142P ARG* 3.2 10.7 + - + +
144P ARG* 1.3 72.0 - - - +
146P THR* 1.3 64.5 + - - +
147P LYS 3.4 0.2 + - - -
148P THR* 3.4 11.3 - - - +
149P LEU* 3.2 19.1 + - - +
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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
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131P VAL* 2.9 32.6 + - + +
132P THR* 5.6 1.3 - - + -
137P TYR* 3.0 14.6 + - - +
142P ARG 3.1 8.7 + - - -
143P ALA 3.3 7.2 + - - -
145P LEU* 1.3 77.3 - - - +
147P LYS* 1.3 61.9 + - - +
149P LEU* 3.0 18.3 + - + +
150P ALA* 3.1 12.1 + - - +
165P ILE* 3.8 29.7 - - + +
166P LEU* 5.7 0.6 - - + +
169P LEU* 4.2 20.9 - - + -
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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 3.1 12.4 + - - +
144P ARG* 3.0 18.5 + - + +
146P THR* 1.3 74.6 - - - +
148P THR* 1.4 57.8 + - - +
150P ALA* 3.3 11.1 - - + +
151P THR* 3.0 32.9 + - - +
166P LEU* 4.5 12.1 - - + -
169P LEU* 4.7 6.5 - - + +
184P GLU* 4.8 19.1 + - - +
185P PHE* 3.9 41.3 - - + +
188P GLU* 5.4 10.8 + - - +
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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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113P GLU* 4.2 18.3 + - - +
121P LYS* 4.0 26.5 - - - +
125P ILE* 5.9 1.8 - - + -
144P ARG 2.9 15.7 + - - -
145P LEU* 3.4 14.6 + - - +
147P LYS* 1.4 75.1 - - - +
149P LEU* 1.3 63.2 + - - -
151P THR* 3.1 13.5 + - - -
152P ILE* 3.1 24.9 + - + +
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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
----------------------------------------------------------
122P LEU* 5.0 6.3 - - + -
125P ILE* 3.9 30.2 - - + +
126P ASP* 4.0 17.9 - - - +
131P VAL* 4.8 11.2 - - + -
132P THR* 4.5 19.7 - - + -
145P LEU 3.2 7.8 + - - +
146P THR* 3.0 11.7 + - + +
148P THR* 1.3 77.8 - - - +
150P ALA* 1.4 62.8 - - - +
152P ILE* 3.2 19.7 + - - +
153P LYS* 3.3 30.2 + - + +
165P ILE* 4.6 24.0 - - + -
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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
----------------------------------------------------------
146P THR 3.1 9.2 + - - +
147P LYS* 3.3 11.9 - - + +
148P THR 3.3 0.2 - - - -
149P LEU* 1.4 74.6 - - - +
151P THR* 1.3 63.8 + - - +
153P LYS* 3.1 12.1 + - - +
154P GLU* 3.1 24.6 + - - +
162P ALA* 4.1 5.0 - - + +
165P ILE* 4.4 13.7 - - + +
166P LEU* 3.8 39.9 - - + -
188P GLU* 6.2 0.2 - - + -
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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
----------------------------------------------------------
147P LYS* 3.0 25.8 + - - +
148P THR* 3.1 15.5 - - - -
150P ALA* 1.3 75.6 - - - +
152P ILE* 1.3 65.0 + - + +
154P GLU* 3.3 35.1 + - - +
155P GLN* 3.7 6.6 + - - +
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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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118P LEU* 3.9 24.5 - - + +
119P PRO* 6.4 0.7 - - + -
121P LYS* 3.9 31.2 - - - +
122P LEU* 4.2 29.6 - - + -
125P ILE* 5.2 2.5 - - + -
148P THR* 3.1 17.8 + - + +
149P LEU* 3.2 13.0 + - - +
151P THR* 1.3 76.5 - - + +
153P LYS* 1.4 63.1 + - + +
154P GLU 3.5 0.3 + - - -
155P GLN* 3.6 10.0 - - - +
156P ASN* 3.3 29.4 + - - +
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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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122P LEU* 4.5 26.1 - - + +
149P LEU* 3.4 27.4 - - + +
150P ALA* 3.1 10.0 + - - +
152P ILE* 1.4 79.5 - - - +
154P GLU* 1.4 63.1 + - - +
156P ASN* 3.3 17.8 + - - +
158P ASP* 3.2 63.4 + - - +
161P GLU* 4.3 19.7 - - + -
162P ALA* 4.2 11.2 - - + +
165P ILE* 5.8 1.1 - - + -
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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 14.7 + - - +
151P THR* 3.3 30.4 + - - +
153P LYS* 1.4 76.6 - - - +
155P GLN* 1.4 62.0 + - - +
157P GLY* 3.1 15.4 + - - -
158P ASP 4.2 5.7 + - - +
159P VAL* 5.9 1.5 - - - +
162P ALA* 4.8 9.6 - - + -
188P GLU* 3.2 34.8 - - + +
191P ARG* 5.3 3.8 + - - -
192P LEU* 5.0 7.5 - - + +
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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 3.7 5.8 + - - +
152P ILE* 3.6 12.1 - - - +
154P GLU* 1.4 76.5 - - - +
156P ASN* 1.3 75.5 + - - +
157P GLY* 3.3 1.7 + - - -
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Residues in contact with ASN 156 (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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122P LEU* 4.8 7.3 - - - +
152P ILE* 3.3 33.1 + - - +
153P LYS* 3.6 12.9 - - - +
154P GLU 3.2 0.8 - - - -
155P GLN* 1.3 91.5 + - - +
157P GLY* 1.4 54.8 + - - +
158P ASP* 3.2 35.7 + - - +
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Residues in contact with GLY 157 (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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154P GLU 3.1 13.7 + - - -
155P GLN 3.1 2.6 - - - -
156P ASN* 1.4 75.7 - - - +
158P ASP* 1.3 63.8 + - - +
159P VAL* 3.1 18.3 + - - +
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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
------------------------------------------------------------
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