Contacts of the helix formed by residues 165 - 180 (chain A) in PDB entry 1LD7
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 ASN 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 3.1 36.4 + - - +
129A ALA* 3.6 7.7 - - - +
162A GLN* 3.6 24.3 + - + +
163A PRO 3.4 1.8 - - - -
164A LYS* 1.3 77.4 - - - +
166A TYR* 1.3 63.1 + - - +
167A GLN* 2.7 39.3 + - - +
168A VAL* 2.9 25.2 + - + +
169A TRP* 3.2 22.2 - - - -
201A HIS* 4.7 1.3 - - - -
1003B U66 6.1 1.1 - - - -
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Residues in contact with TYR 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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164A LYS 4.9 1.8 - - - -
165A ASN* 1.3 72.0 + - - +
167A GLN* 1.3 76.9 + - - +
169A TRP* 3.4 5.1 + - - +
170A HIS* 3.2 22.5 + - - +
201A HIS* 3.4 35.2 - + - -
698B GLU* 3.8 21.5 - - + +
700B ASP* 3.8 6.5 - - - -
702B ARG* 3.2 36.3 + - - -
751B TYR* 2.8 24.6 + - - -
1002B FPP 3.7 4.2 - - - +
1003B U66 3.3 62.8 + + + -
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA 4.2 0.9 - - - +
129A ALA* 3.3 30.8 + - - +
131A TYR* 3.9 26.4 - - + +
134A TRP* 3.5 35.9 - - + +
138A ARG* 4.4 3.6 + - - +
165A ASN* 2.7 19.5 + - - +
166A TYR* 1.3 84.0 + - - +
168A VAL* 1.3 60.6 + - - +
170A HIS* 3.3 6.8 + - - +
171A HIS* 2.9 30.4 + - - +
649B HIS* 4.8 9.3 + - - -
694B HIS* 5.6 2.7 + - - +
698B GLU* 4.5 10.4 + - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 4.7 4.7 - - + -
134A TRP* 3.7 15.0 - - + -
155A ILE* 3.5 20.5 - - + +
158A ILE* 3.4 27.8 - - + -
159A ILE* 3.7 23.1 - - + +
162A GLN* 3.5 21.5 - - + +
165A ASN* 2.9 41.6 + - + +
167A GLN* 1.3 72.7 - - - +
169A TRP* 1.3 70.2 + - + +
171A HIS* 3.4 1.4 + - - -
172A ARG* 3.1 18.5 + - - +
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Residues in contact with TRP 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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159A ILE* 3.5 28.0 - - + +
163A PRO 2.8 26.0 + - - -
165A ASN 3.2 22.2 - - - -
166A TYR* 3.4 7.0 + - - +
167A GLN 3.3 0.4 - - - -
168A VAL* 1.3 86.3 - - + +
170A HIS* 1.3 62.9 + - - +
172A ARG* 3.3 5.5 + - - +
173A ARG* 3.0 22.0 + - - +
188A PHE* 3.8 27.6 - + - -
189A ILE* 4.6 5.2 - - + -
192A ILE* 4.1 13.7 - - + -
201A HIS* 3.3 29.8 - + + +
202A ALA* 3.7 27.8 - - + -
205A HIS* 3.6 50.9 + + + +
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Residues in contact with HIS 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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138A ARG* 3.9 12.2 + - - +
166A TYR 3.2 17.3 + - - +
167A GLN* 3.3 6.2 + - - +
169A TRP* 1.3 73.1 - - - +
171A HIS* 1.3 65.6 + - - +
173A ARG* 3.2 19.8 + - - +
174A VAL* 3.0 43.7 + - + +
694B HIS* 5.5 0.8 + - - -
696B GLY 2.8 31.6 + - - -
697B GLY* 3.4 16.8 + - - -
698B GLU* 3.5 37.3 + - + +
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Residues in contact with HIS 171 (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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134A TRP* 3.5 29.9 - + + -
137A ARG* 4.6 4.3 - - - -
138A ARG* 3.2 46.7 + - + +
141A LEU* 3.7 18.4 - - + -
151A GLU* 2.7 34.2 + - - +
154A TYR* 5.3 0.4 - + - -
155A ILE* 3.7 17.9 - - + -
167A GLN 2.9 17.0 + - - +
168A VAL 3.6 4.9 - - - +
169A TRP 3.3 0.2 - - - -
170A HIS* 1.3 75.1 + - - +
172A ARG* 1.3 62.8 + - - +
174A VAL* 3.3 4.7 + - - +
175A LEU* 3.1 38.1 + - + +
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Residues in contact with ARG 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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152A MET* 3.7 16.9 + - - +
155A ILE* 3.7 28.2 - - + +
156A THR* 3.0 28.7 + - - +
159A ILE* 3.8 15.5 - - + +
168A VAL 3.1 10.6 + - - +
169A TRP* 3.6 9.9 - - - +
170A HIS 3.2 0.2 - - - -
171A HIS* 1.3 77.0 - - - +
173A ARG* 1.3 65.0 + - - +
175A LEU* 3.2 8.4 + - - +
176A VAL* 3.0 27.0 + - + +
184A GLN* 4.2 9.9 + - - +
185A GLU* 2.8 39.8 + - - +
188A PHE* 3.3 46.7 - - - +
205A HIS* 3.9 10.3 - - + +
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Residues in contact with ARG 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 TRP 3.0 11.9 + - - +
170A HIS* 3.2 24.3 + - + +
172A ARG* 1.3 75.3 - - - +
174A VAL* 1.3 65.5 + - + +
176A VAL* 3.2 3.3 + - - +
177A GLU* 2.9 47.9 + - - +
204A GLN* 5.8 3.2 - - - +
205A HIS* 3.8 18.8 - - + +
208A TRP* 3.4 56.2 - - + +
699B VAL* 6.2 3.9 - - - +
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Residues in contact with VAL 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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138A ARG* 4.0 21.3 - - + +
170A HIS* 3.0 46.5 + - + +
171A HIS 3.5 8.7 - - - +
172A ARG 3.2 0.2 - - - -
173A ARG* 1.3 76.6 - - + +
175A LEU* 1.3 56.6 + - + +
177A GLU* 3.2 17.0 + - - +
178A TRP* 2.8 67.2 + - + +
696B GLY 5.1 0.2 - - - +
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Residues in contact with LEU 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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141A LEU* 4.1 15.3 - - + -
148A LEU* 4.3 9.6 - - + -
151A GLU* 3.5 49.1 - - + +
152A MET* 3.9 23.1 - - + +
155A ILE* 4.0 10.1 - - + -
171A HIS* 3.1 31.8 + - + +
172A ARG* 3.2 6.3 + - - +
174A VAL* 1.3 77.7 - - + +
176A VAL* 1.3 55.8 - - - +
178A TRP* 3.2 21.2 + - + +
179A LEU* 2.9 38.3 + - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 4.0 12.6 - - + -
172A ARG* 3.0 20.1 + - + +
173A ARG* 3.6 6.5 - - - +
175A LEU* 1.3 75.7 - - - +
177A GLU* 1.3 53.5 + - - +
179A LEU* 4.6 3.1 - - - +
180A ARG* 2.6 32.7 + - - -
181A ASP 3.4 20.4 + - - +
182A PRO* 4.2 4.9 - - + -
185A GLU* 3.5 34.3 - - + +
205A HIS* 4.8 2.5 - - - +
208A TRP* 3.9 10.8 - - + -
213A PHE* 3.8 28.3 - - + -
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Residues in contact with GLU 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 ARG* 2.9 48.4 + - - +
174A VAL* 3.2 22.4 + - - +
176A VAL* 1.3 74.6 - - - +
178A TRP* 1.3 69.9 + - + +
180A ARG* 3.4 31.8 + - - +
208A TRP* 3.5 21.4 + - + -
213A PHE* 5.2 1.6 - - - -
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Residues in contact with TRP 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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138A ARG* 3.5 38.6 - - + -
141A LEU* 4.0 29.8 - - + -
142A LYS* 4.9 16.8 - - + -
148A LEU* 3.7 32.9 - - + +
174A VAL* 2.8 37.3 + - + +
175A LEU* 3.2 16.1 + - + +
177A GLU* 1.3 78.7 - - + +
179A LEU* 1.3 60.6 + - - +
180A ARG* 4.8 2.4 - - - +
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Residues in contact with LEU 179 (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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148A LEU* 3.6 35.9 - - + -
149A HIS* 3.9 36.1 - - + +
152A MET* 3.9 29.4 - - + -
175A LEU* 2.9 20.3 + - + +
176A VAL* 4.1 2.5 - - - +
178A TRP* 1.3 76.2 - - - +
180A ARG* 1.3 71.1 + - - +
181A ASP* 3.1 22.3 + - + +
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Residues in contact with ARG 180 (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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176A VAL 2.6 18.5 + - - -
177A GLU* 3.4 23.3 + - - +
178A TRP 3.4 2.6 - - - +
179A LEU* 1.3 77.0 - - - +
181A ASP* 1.3 54.7 + - - +
182A PRO* 3.7 6.4 - - - +
212A GLU* 2.5 40.8 + - - +
213A PHE* 3.5 39.0 - - - -
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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