Contacts of the helix formed by residues 177 - 188 (chain A) in PDB entry 1LDJ
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 LYS 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ARG 5.1 3.8 - - - +
174A PRO* 3.5 5.8 + - + +
176A ASN* 1.3 89.3 - - + +
178A GLN* 1.2 85.0 + - + +
179A VAL 2.8 1.4 + - - -
180A THR 3.4 1.9 + - - -
181A ASN* 3.1 37.2 + - - +
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Residues in contact with GLN 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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109A ASP* 4.8 13.3 - - - +
111A MET* 3.3 43.4 + - + +
115A VAL* 5.9 0.9 - - + -
174A PRO* 3.7 13.4 + - + +
177A LYS* 1.2 90.0 - - + +
179A VAL* 1.3 58.8 + - + +
181A ASN* 3.8 8.6 - - + +
182A ALA* 2.8 26.7 + - - +
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Residues in contact with VAL 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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115A VAL* 3.3 37.7 - - + -
116A LEU* 5.8 0.7 - - - -
119A TYR* 3.9 21.1 - - + -
174A PRO 3.5 0.4 - - - +
175A LEU* 1.4 71.9 - - + +
177A LYS 2.8 4.4 + - - +
178A GLN* 1.3 76.7 - - - +
180A THR* 1.3 66.7 + - - +
182A ALA* 2.9 19.8 - - - +
183A VAL* 3.0 7.9 + - + +
204A VAL* 4.0 11.4 - - + -
208A TYR* 3.6 13.2 - - - +
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Residues in contact with THR 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 ASN 3.4 12.8 + - - -
177A LYS 3.4 1.7 + - - -
179A VAL* 1.3 78.0 - - - +
181A ASN* 1.3 65.6 + - - +
183A VAL* 2.6 31.9 + - - +
184A LEU* 3.0 15.1 + - + +
208A TYR* 2.7 29.6 + - - -
231A SER 3.1 27.5 + - - +
232A PHE* 3.8 19.9 - - + +
235A GLN* 4.0 15.7 - - + -
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Residues in contact with ASN 181 (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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111A MET* 6.0 4.0 - - + -
112A ASP* 4.9 1.1 - - - +
176A ASN 5.1 0.2 + - - -
177A LYS* 3.1 33.6 + - - +
178A GLN* 3.8 11.2 - - + +
179A VAL 3.2 0.4 - - - -
180A THR* 1.3 85.9 - - - +
182A ALA* 1.3 61.8 + - - +
184A LEU* 3.7 17.6 + - - +
185A LYS* 3.1 31.6 + - - +
235A GLN* 5.1 7.3 - - - +
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Residues in contact with ALA 182 (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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112A ASP* 3.1 40.3 + - + +
113A GLU* 4.7 3.1 - - - +
115A VAL* 3.7 13.0 - - + -
116A LEU* 5.3 3.4 - - + +
178A GLN 2.8 16.1 + - - +
179A VAL 2.9 13.7 - - - +
181A ASN* 1.3 72.3 - - - +
183A VAL* 1.3 61.3 + - + +
185A LYS* 3.1 2.8 + - - +
186A LEU* 2.9 33.4 + - + +
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Residues in contact with VAL 183 (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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179A VAL* 3.0 13.8 + - + +
180A THR* 2.6 18.8 + - - +
182A ALA* 1.3 69.1 - - + +
184A LEU* 1.3 53.5 + - - +
186A LEU* 2.8 11.5 + - - +
187A ILE* 2.7 36.7 + - + +
201A ILE* 3.4 36.3 - - + -
204A VAL* 3.5 36.3 - - + -
205A VAL* 5.4 0.2 - - + -
232A PHE* 3.6 25.8 - - + -
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Residues in contact with LEU 184 (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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180A THR* 3.5 9.6 - - + +
181A ASN* 3.8 23.1 - - - +
183A VAL* 1.3 75.9 - - - +
185A LYS* 1.3 54.6 + - + +
187A ILE* 3.6 8.3 - - + +
188A GLU* 2.7 35.7 + - - +
232A PHE* 3.9 18.4 - - + -
235A GLN* 3.1 39.5 - - + +
236A PHE* 3.7 23.1 - - + -
239A ASP* 3.8 30.5 - - + +
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Residues in contact with LYS 185 (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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111A MET* 5.6 4.5 - - - -
112A ASP* 3.4 23.3 - - - +
181A ASN* 3.1 22.9 + - - +
182A ALA 3.1 11.8 + - - +
183A VAL 3.1 0.6 - - - -
184A LEU* 1.3 80.8 - - + +
186A LEU* 1.3 62.8 + - + +
188A GLU* 3.5 31.5 + - - +
189A LYS* 4.2 4.3 + - - +
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Residues in contact with LEU 186 (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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113A GLU* 4.0 18.4 - - + -
116A LEU* 3.5 35.0 - - + -
182A ALA 2.9 26.5 - - - +
183A VAL* 2.8 7.5 + - - +
185A LYS* 1.3 78.8 - - + +
187A ILE* 1.3 56.3 + - - +
188A GLU 3.0 1.6 - - - -
189A LYS* 2.7 40.4 + - + +
196A ILE* 4.1 32.9 - - + +
200A LEU* 4.5 2.2 - - + -
201A ILE* 3.8 20.2 - - + -
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Residues in contact with ILE 187 (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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183A VAL* 2.7 27.0 + - + +
184A LEU* 3.7 10.1 - - + +
186A LEU* 1.3 66.5 - - - +
188A GLU* 1.3 53.9 + - - +
189A LYS 2.5 18.1 + - - -
190A GLU* 2.9 48.4 + - + +
196A ILE* 5.8 0.7 - - - -
201A ILE* 3.7 19.0 - - + +
232A PHE* 3.7 21.5 - - + -
236A PHE* 3.7 39.0 - - + -
240A THR* 4.7 1.8 - - - +
274A ARG* 6.5 0.9 - - + -
278A TYR* 5.8 7.0 - - + +
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Residues in contact with GLU 188 (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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184A LEU 2.7 20.7 + - - +
185A LYS* 3.5 28.3 + - - +
186A LEU 3.0 0.6 - - - -
187A ILE* 1.3 71.5 - - - +
189A LYS* 1.3 56.2 + - - +
190A GLU* 2.9 16.8 + - - -
191A ARG* 3.1 24.7 + - - +
239A ASP* 5.3 6.6 - - - +
242A ARG* 4.5 15.1 + - - -
243A PHE* 3.8 13.3 - - + -
246A ARG* 4.8 9.4 + - - -
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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