Contacts of the helix formed by residues 188 - 197 (chain A) in PDB entry 2NLL
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 GLN 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A PHE* 3.8 15.1 - - + -
169A TYR* 3.1 59.1 + - + -
185A ASN* 4.8 10.5 - - - +
186A ARG 5.8 0.2 - - - -
187A CYS* 1.3 72.7 - - - +
189A TYR* 1.3 67.1 + - - +
191A ARG* 3.8 0.7 - - - -
192A TYR 2.9 17.2 + - - -
531D A 4.2 10.3 + - - -
532D T 3.4 23.7 + - - +
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Residues in contact with TYR 189 (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 TYR* 3.5 32.2 - - + +
170A THR* 3.7 5.5 + - + +
171A CYS* 3.3 39.7 - - + +
175A LYS* 3.9 26.0 - - + +
187A CYS* 3.3 7.0 - - - -
188A GLN* 1.3 77.8 - - - +
190A CYS* 1.3 65.5 + - - +
192A TYR* 3.0 4.8 + - - +
193A GLN* 2.8 66.4 + - + +
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Residues in contact with CYS 190 (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 CYS* 4.0 0.7 - - - -
175A LYS* 2.9 53.1 + - + +
176A ASP 3.9 0.9 - - - -
177A CYS* 3.4 24.5 - - + +
179A ILE* 4.2 4.0 - - + -
187A CYS* 3.2 6.3 - - + -
189A TYR* 1.3 80.2 - - - +
191A ARG* 1.3 53.2 + - - +
194A LYS* 2.7 38.3 + - - +
251A ZN 2.3 36.8 - - - -
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Residues in contact with ARG 191 (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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137A ILE* 4.3 5.2 - - + +
154A GLY* 3.1 6.7 - - - -
155A CYS* 3.1 46.8 - - - +
158A PHE* 3.6 43.8 - - + +
179A ILE* 3.7 24.1 - - + +
184A ARG* 3.4 33.0 + - - +
185A ASN* 3.1 31.1 - - - +
187A CYS 3.2 20.5 + - - +
188A GLN* 4.0 1.1 - - - +
189A TYR 3.2 0.2 - - - -
190A CYS* 1.3 76.2 - - - +
192A TYR* 1.3 57.6 + - - +
194A LYS* 3.5 2.9 - - - +
195A CYS* 3.0 26.7 + - - -
532D T 5.0 0.4 - - - -
533D G 3.1 12.1 + - - -
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Residues in contact with TYR 192 (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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158A PHE* 3.8 6.0 - + + -
159A PHE* 3.2 35.0 - + - -
162A THR* 3.3 33.0 - - + -
163A VAL* 3.3 20.0 - - + +
166A ASP* 3.8 9.1 + - - -
167A LEU 6.0 0.7 - - - -
169A TYR* 3.6 19.5 - + + -
188A GLN 2.9 18.8 + - - +
189A TYR 3.5 2.0 - - - +
191A ARG* 1.3 73.6 - - - +
193A GLN* 1.3 74.6 + - - +
194A LYS 3.0 0.9 - - - -
195A CYS* 2.7 29.1 + - - +
196A LEU* 3.1 26.2 + - + +
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Residues in contact with GLN 193 (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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175A LYS* 3.9 17.3 - - + +
189A TYR* 2.8 62.6 + - + +
190A CYS 4.0 0.2 - - - +
192A TYR* 1.3 89.2 - - - +
194A LYS* 1.3 53.0 + - - +
195A CYS 3.0 0.3 + - - -
196A LEU* 3.2 29.3 + - + +
197A ALA* 2.7 39.1 + - + +
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Residues in contact with LYS 194 (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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136A ALA 3.7 8.3 - - - -
137A ILE* 2.7 64.6 + - + +
175A LYS* 4.0 11.4 - - - +
178A LEU* 5.5 3.0 - - - +
179A ILE* 3.8 25.6 + - + +
190A CYS 2.7 25.7 + - - +
191A ARG* 3.5 8.7 - - - +
193A GLN* 1.3 74.2 - - - +
195A CYS* 1.3 61.3 + - - +
197A ALA* 4.0 6.1 - - + -
198A MET* 3.2 37.3 + - + +
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Residues in contact with CYS 195 (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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137A ILE* 3.6 18.8 - - - +
155A CYS* 4.3 11.4 - - - -
158A PHE* 4.5 10.8 - - - -
159A PHE* 3.2 38.1 - - + -
191A ARG 3.0 18.4 + - - +
192A TYR 2.7 19.8 + - - +
194A LYS* 1.3 75.3 - - - +
196A LEU* 1.3 59.0 + - - +
197A ALA 3.3 0.2 + - - -
198A MET 3.4 1.6 + - - -
199A GLY 3.4 11.6 + - - +
200A MET* 3.3 33.9 - - - +
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Residues in contact with LEU 196 (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 PHE* 4.2 7.1 - - + -
192A TYR* 3.1 37.8 + - + +
193A GLN* 3.3 37.7 - - - +
195A CYS* 1.3 78.8 - - - +
197A ALA* 1.3 69.2 - - + +
199A GLY* 3.2 12.1 + - - -
200A MET* 4.2 18.8 + - - +
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Residues in contact with ALA 197 (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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175A LYS* 5.5 3.4 - - - +
193A GLN* 2.7 26.2 + - + +
194A LYS* 3.7 8.3 - - + +
196A LEU* 1.3 78.0 - - + +
198A MET* 1.3 69.8 + - + +
199A GLY* 3.0 9.0 + - - -
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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