Contacts of the helix formed by residues 162 - 178 (chain A) in PDB entry 2LDX
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 CYS 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASP* 5.4 0.4 - - - -
161A GLY* 1.3 76.7 - - - -
163A ASN* 1.3 64.7 + - - +
164A LEU 2.8 3.9 + - - -
165A ASP* 2.9 23.7 + - + +
166A SER* 2.4 35.6 + - - +
188A VAL* 3.4 25.4 - - + +
189A LEU* 4.4 3.1 - - - -
190A GLY 4.1 8.3 - - - -
191A GLU 4.1 20.0 - - - +
192A HIS 4.3 1.1 - - - -
271A PRO* 4.1 4.2 + - + -
289A SER* 2.7 30.8 + - - +
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Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A SER 3.3 10.9 + - - +
162A CYS* 1.3 79.2 - - - +
164A LEU* 1.3 63.8 + - - +
166A SER* 3.6 2.6 + - - -
167A ALA* 3.1 21.3 + - - +
254A SER* 2.9 32.3 + - - +
257A ASP* 3.9 7.2 + - - +
258A LEU* 3.1 28.2 - - + +
270A HIS* 3.3 20.6 + - - -
271A PRO* 3.2 34.0 + - - +
272A VAL* 4.8 0.2 - - + -
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A SER* 4.6 4.9 - - - +
161A GLY 4.1 12.8 - - - +
163A ASN* 1.3 75.8 - - - +
165A ASP* 1.3 50.5 + - - +
167A ALA* 2.9 12.8 + - - +
168A ARG* 2.8 60.2 + - - +
192A HIS* 3.2 33.4 - - + +
247A THR* 6.1 0.4 - - - +
250A ALA* 4.1 22.0 - - + +
251A ILE* 3.7 37.2 - - + +
254A SER* 4.0 12.3 + - - +
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A CYS* 2.9 29.1 + - + +
164A LEU* 1.3 75.9 - - - +
166A SER* 1.3 52.7 + - - +
168A ARG* 2.8 22.8 + - - +
169A PHE* 2.6 37.3 + - - +
188A VAL* 4.8 10.1 - - + -
191A GLU 4.5 0.3 - - - +
192A HIS* 2.6 44.7 + - - -
193A GLY 4.9 4.2 + - - +
196A SER* 4.9 7.1 + - - -
233A VAL* 4.2 18.2 - - + +
234A VAL* 5.9 1.7 - - - -
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A CYS 2.4 29.2 + - - -
163A ASN 3.6 3.8 - - - -
165A ASP* 1.3 73.7 - - - +
167A ALA* 1.3 51.8 + - - +
169A PHE* 3.2 11.6 - - - +
170A ARG* 2.8 39.5 + - - +
186A GLY 4.5 8.2 - - - +
187A TRP* 4.9 2.2 - - - -
188A VAL* 3.6 29.9 + - - +
271A PRO* 3.6 18.4 - - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 3.1 15.7 + - - +
164A LEU* 2.9 14.3 + - - +
166A SER* 1.3 72.4 - - - +
168A ARG* 1.3 66.0 + - - +
169A PHE 3.0 1.6 - - - -
170A ARG* 3.3 2.5 + - - +
171A TYR* 2.9 24.3 + - - +
254A SER* 6.3 1.1 - - - -
66C HIS 4.3 7.8 - - - +
69C LEU* 3.4 38.6 - - + +
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 2.8 47.3 + - + +
165A ASP* 3.1 27.3 + - - +
167A ALA* 1.3 76.3 - - - +
169A PHE* 1.3 55.1 + - - +
171A TYR* 3.2 21.4 - - - +
172A LEU* 3.3 17.3 + - + +
192A HIS* 4.7 6.3 - - - -
233A VAL* 3.9 29.4 + - + +
236A GLY 4.5 1.6 - - - -
237A GLY* 4.4 15.3 - - - -
240A VAL* 4.6 6.7 - - - +
247A THR* 4.5 14.1 + - - -
250A ALA* 4.8 7.1 - - - +
63C ASP* 5.5 1.2 + - - -
66C HIS* 2.8 64.2 + - + +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASP 2.6 12.2 + - - +
166A SER* 3.2 10.1 - - - +
167A ALA 3.0 0.2 - - - -
168A ARG* 1.3 71.7 - - - +
170A ARG* 1.3 65.1 + - - +
171A TYR 2.7 5.4 + - - -
172A LEU* 3.0 4.0 + - - +
173A ILE* 2.8 40.9 + - + +
186A GLY* 3.5 22.2 - - - -
187A TRP 3.5 23.8 - - - -
188A VAL* 3.1 31.0 - - + -
198A PRO* 3.9 15.7 - - + -
199A ILE 5.0 0.2 - - - -
200A TRP* 4.4 13.9 - + - -
203A VAL* 4.8 3.6 - - + -
229A VAL* 3.4 28.0 - - + -
230A HIS* 4.9 2.5 - - - -
233A VAL* 3.7 26.4 - - + +
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A SER* 2.8 25.9 + - - +
167A ALA* 3.9 3.8 - - - +
169A PHE* 1.3 73.3 - - - +
171A TYR* 1.3 67.3 + - - +
173A ILE* 2.9 21.1 - - + +
174A GLY 3.1 3.3 + - - -
181A PRO* 2.6 51.1 + - + +
182A THR* 3.1 22.0 + - - +
184A CYS 2.5 45.6 + - - +
185A HIS* 3.8 14.4 + - - +
186A GLY* 4.0 22.0 - - - +
187A TRP* 5.8 6.9 - - - -
69C LEU* 3.4 22.8 - - + +
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA 2.9 12.5 + - - +
168A ARG 3.2 13.2 - - - +
169A PHE 2.7 1.8 + - - -
170A ARG* 1.3 84.0 - - - +
172A LEU* 1.3 93.2 + - + +
174A GLY* 2.7 9.4 + - - -
175A GLU* 2.9 41.1 + - + +
181A PRO* 3.9 9.2 - - + +
62C LEU* 4.9 5.5 - - + +
65C GLN* 3.2 48.8 + - + +
66C HIS* 4.0 35.9 - + - +
68C SER* 3.9 17.5 - - - -
69C LEU 5.7 0.7 - - - +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ARG* 3.5 10.8 - - + +
169A PHE 3.0 4.5 + - - +
171A TYR* 1.3 99.4 - - + +
173A ILE* 1.3 58.6 - - - +
175A GLU* 2.6 40.7 + - - +
176A LYS* 3.4 6.9 + - - +
229A VAL* 3.2 40.2 - - + +
232A GLN* 2.9 46.4 - - + +
233A VAL* 3.4 22.9 - - + +
62C LEU* 6.5 0.2 - - + -
66C HIS* 5.1 8.5 - - + +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE* 2.8 46.0 + - + +
170A ARG* 2.9 37.2 - - + +
172A LEU* 1.3 76.3 - - - +
174A GLY* 1.3 58.9 + - - +
176A LYS* 3.1 21.0 + - - +
177A LEU* 3.8 14.0 + - + +
184A CYS* 4.0 20.2 - - + -
185A HIS 4.7 6.7 - - - +
186A GLY* 4.8 1.1 - - - -
200A TRP* 4.6 4.3 - - + -
203A VAL* 4.1 24.2 - - + -
213A LEU* 6.3 1.3 - - + -
226A TRP* 4.3 20.4 - - + -
229A VAL* 3.6 15.8 - - + +
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Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ARG 3.1 2.4 + - - -
171A TYR 2.7 13.4 + - - -
173A ILE* 1.3 73.6 - - - +
175A GLU* 1.3 59.0 + - - -
176A LYS 2.9 7.7 + - - -
177A LEU* 4.1 2.9 - - - -
178A GLY* 3.2 19.9 + - - -
179A VAL 3.3 27.3 + - - +
181A PRO* 5.3 0.9 - - - -
184A CYS* 3.7 12.8 - - - -
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A TYR* 2.9 39.4 + - + +
172A LEU* 2.6 30.4 + - - +
174A GLY* 1.3 73.0 - - - +
176A LYS* 1.3 65.7 + - + +
178A GLY* 4.6 3.3 + - - -
232A GLN* 3.7 22.0 + - - -
65C GLN* 5.3 0.3 + - - -
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Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.4 6.1 + - - +
173A ILE 3.1 8.6 + - - +
174A GLY 2.9 2.8 - - - -
175A GLU* 1.3 89.6 - - - +
177A LEU* 1.3 60.6 + - - +
178A GLY 3.4 1.1 - - - -
225A HIS 5.6 2.0 - - - -
226A TRP* 3.4 41.4 - - + +
228A ASN* 5.8 2.0 - - - +
229A VAL* 3.5 36.8 - - - +
232A GLN* 5.8 3.6 + - - +
4C LYS* 3.3 17.6 - - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ILE* 4.1 13.9 - - + +
174A GLY 3.6 1.9 + - - +
176A LYS* 1.3 76.2 - - - +
178A GLY* 1.3 62.7 + - - +
179A VAL* 4.0 16.0 - - + +
184A CYS* 4.1 15.9 - - + -
205A VAL* 3.3 38.8 - - + -
213A LEU* 5.0 5.8 - - + -
226A TRP* 4.3 15.0 - - + -
3C VAL* 4.2 9.6 - - + -
4C LYS* 2.3 60.5 - - - +
7C LEU* 5.0 6.3 - - + -
8C ILE* 4.6 12.3 - - + +
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLY 3.2 9.5 + - - -
175A GLU 5.0 2.7 - - - -
176A LYS 3.4 2.0 - - - -
177A LEU* 1.3 80.1 - - - +
179A VAL* 1.3 64.8 - - - +
267B LYS* 3.7 34.1 - - - +
293B VAL* 4.4 7.8 - - - +
301B ASP* 5.1 3.5 - - - +
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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