Contacts of the helix formed by residues 153 - 164 (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 GLU 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASP* 5.5 0.2 + - - -
143A SER* 3.1 30.6 + - - -
146A HIS* 4.1 2.1 - - - -
152A CYS* 1.3 73.8 - - - +
154A GLY* 1.3 55.6 + - - +
156A LYS* 3.0 37.3 + - + +
157A GLY* 2.8 26.9 + - - -
533D G 4.2 8.9 - - - +
534D A 3.9 30.7 + - + +
535D C 3.2 41.1 + - - +
536D C 4.9 2.6 + - - -
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Residues in contact with GLY 154 (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 CYS* 3.0 9.8 - - - -
153A GLU* 1.3 76.9 - - - +
155A CYS* 1.3 60.2 + - - +
158A PHE* 2.8 30.8 + - - +
161A ARG* 4.5 2.4 + - - -
184A ARG* 5.3 2.5 - - - -
191A ARG* 3.1 7.5 + - - -
533D G 3.7 35.7 + - - +
534D A 4.9 1.6 + - - -
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Residues in contact with CYS 155 (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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135A CYS* 3.7 9.9 - - - -
137A ILE* 3.7 25.1 - - + -
138A CYS* 4.0 4.7 - - - -
151A SER* 4.5 6.5 - - - -
152A CYS* 2.9 8.8 - - - +
154A GLY* 1.3 72.1 - - - +
156A LYS* 1.3 59.3 + - - +
158A PHE* 3.7 5.3 - - - +
159A PHE* 2.9 31.9 + - - +
191A ARG* 3.1 29.3 - - - +
195A CYS* 4.3 8.2 - - - -
200A MET* 4.7 1.0 - - - +
250A ZN 2.3 35.7 - - - -
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A HIS* 4.2 31.7 + - + +
147A TYR* 4.1 13.6 - - + +
151A SER* 4.4 6.0 + - - -
152A CYS 2.6 24.6 + - - +
153A GLU* 3.0 40.7 + - + +
155A CYS* 1.3 69.6 - - - +
157A GLY* 1.3 55.4 + - - +
159A PHE* 3.1 4.4 + - - +
160A LYS* 2.6 56.6 + - - +
200A MET* 6.1 0.4 - - - -
503C A 5.1 5.7 + - - +
504C G 3.1 40.7 + - - -
505C G 4.1 2.4 + - - -
535D C 4.0 4.0 - - - +
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Residues in contact with GLY 157 (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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153A GLU 2.8 20.8 + - - -
154A GLY 4.0 0.2 - - - -
156A LYS* 1.3 72.7 - - - +
158A PHE* 1.3 62.9 + - - +
160A LYS* 2.8 28.3 + - - +
161A ARG* 2.8 42.3 + - - +
533D G 4.8 2.7 - - - -
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Residues in contact with PHE 158 (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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154A GLY 2.8 21.0 + - - +
155A CYS* 3.7 5.8 - - - +
157A GLY* 1.3 74.8 - - - +
159A PHE* 1.3 59.8 + - - +
161A ARG* 3.3 19.7 + - - +
162A THR* 2.7 37.7 + - - -
169A TYR* 3.4 36.8 - + - -
188A GLN* 3.8 21.5 - - + -
191A ARG* 3.6 44.0 - - + +
192A TYR* 3.8 20.4 - + - -
195A CYS* 4.5 10.3 - - - -
532D T 3.8 26.2 - - - -
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Residues in contact with PHE 159 (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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147A TYR* 3.2 27.8 - + + -
155A CYS 2.9 19.0 + - - +
156A LYS* 3.8 2.0 - - - +
158A PHE* 1.3 75.1 - - - +
160A LYS* 1.3 66.0 + - - +
161A ARG 3.4 0.2 + - - -
162A THR* 3.6 8.5 + - - -
163A VAL* 3.7 29.2 + - + +
192A TYR* 3.2 36.6 - + - -
195A CYS* 3.2 35.4 - - + -
196A LEU* 4.2 8.5 - - + -
200A MET* 3.0 43.5 - - + -
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Residues in contact with LYS 160 (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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147A TYR* 3.1 27.3 - - - +
153A GLU 5.3 0.2 + - - -
156A LYS* 2.6 37.6 + - - +
157A GLY* 3.1 26.4 - - - +
159A PHE* 1.3 74.3 - - - +
161A ARG* 1.3 67.0 + - + +
164A ARG* 3.5 33.4 + - - +
504C G 6.1 1.3 - - - -
505C G 4.1 14.0 + - + +
506C T 3.8 29.0 + - + -
533D G 5.0 2.2 + - - -
534D A 3.8 12.1 - - - +
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Residues in contact with ARG 161 (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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154A GLY 4.5 2.2 + - - -
157A GLY* 2.8 15.9 + - - +
158A PHE* 3.3 36.5 - - - +
160A LYS* 1.3 87.3 - - + +
162A THR* 1.3 70.2 + - - +
164A ARG* 3.2 4.3 + - - +
165A LYS* 3.0 47.1 + - - +
531D A 5.3 0.9 - - - -
532D T 2.4 86.0 + - - +
533D G 3.2 30.1 + - - -
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Residues in contact with THR 162 (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* 2.7 30.5 + - - -
159A PHE* 4.1 8.1 - - - -
160A LYS 3.6 0.2 - - - -
161A ARG* 1.3 79.2 - - - +
163A VAL* 1.3 66.8 + - - +
165A LYS 3.1 3.4 - - - +
166A ASP* 2.9 39.3 - - - +
169A TYR* 2.8 35.9 + - + -
192A TYR* 3.3 34.5 - - + -
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Residues in contact with VAL 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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159A PHE* 3.7 33.8 + - + +
161A ARG 3.6 0.2 - - - -
162A THR* 1.3 77.5 - - - +
164A ARG* 1.3 66.8 + - - +
166A ASP* 3.1 17.6 - - - +
192A TYR* 3.3 28.0 - - + +
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Residues in contact with ARG 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 LYS* 3.5 25.5 + - - +
161A ARG* 3.2 9.5 + - - +
162A THR 3.1 1.6 + - - -
163A VAL* 1.3 80.8 - - - +
165A LYS* 1.3 58.1 + - + +
166A ASP* 2.6 16.1 + - - +
504C G 4.1 9.5 + - - -
505C G 2.6 38.8 + - - -
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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