Contacts of the helix formed by residues 165 - 177 (chain B) in PDB entry 5NS3
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 THR 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN* 4.2 11.7 - - + +
27A ASN* 3.6 17.3 - - - +
29A TRP* 5.6 0.4 - - - -
30A GLU* 3.5 25.1 - - - +
127B GLY 5.2 2.2 - - - -
129B GLY* 3.7 5.9 - - - +
163B ALA* 3.8 1.7 - - - +
164B GLU* 1.3 80.2 - - - +
166B ASP* 1.3 65.7 + - - +
167B GLU* 3.7 10.6 + - - +
168B GLU* 2.6 40.3 + - - +
169B ALA* 3.2 20.3 + - - +
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Residues in contact with ASP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.4 30.6 - - + +
127B GLY* 3.0 39.7 + - - -
129B GLY 3.1 14.2 + - - -
165B THR* 1.3 72.6 - - - +
167B GLU* 1.3 54.8 + - - +
169B ALA* 3.1 6.8 + - - +
170B ARG* 2.8 48.2 + - - +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 5.1 8.7 + - - -
23B PHE* 4.0 26.4 - - + -
165B THR* 3.2 10.6 + - - +
166B ASP* 1.3 79.0 - - - +
168B GLU* 1.3 63.6 + - + +
170B ARG* 3.4 16.4 + - - +
171B ALA* 3.1 21.3 + - - +
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 5.5 2.3 + - - -
30A GLU* 5.1 2.8 - - - +
19B LEU* 4.8 1.6 - - - +
23B PHE* 4.2 26.5 - - + -
25B TYR* 2.5 41.6 + - - +
32B PRO* 4.1 9.1 - - + +
163B ALA* 3.9 13.4 - - + -
164B GLU* 4.2 8.8 + - - +
165B THR* 2.6 39.7 + - - +
167B GLU* 1.3 78.8 - - + +
169B ALA* 1.3 58.2 + - - +
171B ALA* 3.4 2.8 + - - +
172B LEU* 3.0 27.0 + - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.6 16.2 - - + -
129B GLY* 3.3 29.6 - - - +
161B THR* 4.2 5.8 - - + +
163B ALA* 3.7 10.0 - - + +
165B THR 3.2 12.5 + - - +
166B ASP 3.1 8.2 + - - +
168B GLU* 1.3 72.5 - - - +
170B ARG* 1.3 66.5 + - - +
172B LEU* 3.3 6.4 + - - +
173B LEU* 3.0 28.3 + - + +
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PRO* 3.0 38.7 + - - +
123B ASN* 4.8 5.1 + - - +
125B PHE* 3.6 33.8 - - + +
166B ASP* 2.8 26.6 + - - +
167B GLU* 3.6 23.1 - - - +
168B GLU 3.3 0.2 - - - -
169B ALA* 1.3 77.6 - - - +
171B ALA* 1.3 57.5 + - - +
173B LEU* 3.9 0.7 - - - +
174B GLU* 2.9 59.8 + - + +
180B PHE* 4.5 4.2 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 3.8 4.9 - - + -
22B ARG* 3.7 22.4 - - - +
23B PHE* 3.6 28.9 - - + -
167B GLU 3.1 10.5 + - - +
168B GLU 3.6 7.4 - - - +
169B ALA 3.3 0.2 - - - -
170B ARG* 1.3 76.3 - - - +
172B LEU* 1.3 63.0 + - - +
174B GLU* 3.9 6.2 - - - +
175B LEU* 3.1 31.9 + - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.6 33.9 - - + -
15B VAL* 3.9 11.4 - - + -
19B LEU* 4.0 13.8 - - + +
32B PRO* 3.9 20.4 - - + +
33B ARG* 4.0 7.6 - - - +
34B LEU* 4.1 11.2 - - + +
161B THR* 3.9 35.0 - - + -
168B GLU 3.0 13.8 + - - +
169B ALA* 3.3 7.6 + - - +
171B ALA* 1.3 77.1 - - - +
173B LEU* 1.3 59.1 + - + +
175B LEU* 3.5 2.1 + - - +
176B LEU* 3.0 40.7 + - + +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.8 29.8 - - + -
125B PHE* 4.0 12.6 - - + -
131B TYR* 3.6 34.1 - - + -
159B VAL* 4.1 9.0 - - + -
161B THR* 4.5 7.4 - - + -
169B ALA 3.0 17.7 + - - +
170B ARG 4.0 2.0 - - - +
172B LEU* 1.3 78.4 - - + +
174B GLU* 1.3 64.3 + - - +
176B LEU* 3.3 4.0 + - + -
177B GLY 3.2 5.2 + - - -
178B PHE* 3.0 65.9 + - + -
180B PHE* 4.1 8.3 - - + -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 4.9 7.8 + - - +
122B PRO* 6.1 0.2 - - - +
170B ARG* 2.9 40.3 + - - +
171B ALA* 3.9 8.9 - - - +
173B LEU* 1.3 77.0 - - - +
175B LEU* 1.3 58.9 + - + +
177B GLY* 3.0 20.1 + - - -
178B PHE 4.1 8.7 + - - +
180B PHE* 3.4 29.5 - - + +
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 2.8 22.5 + - - -
15B VAL* 3.4 27.3 - - + +
18B GLU* 3.7 34.8 - - + -
19B LEU* 3.7 28.7 - - + -
22B ARG* 3.9 21.3 - - - +
171B ALA 3.1 21.5 + - - +
174B GLU* 1.3 79.1 - - + +
176B LEU* 1.3 57.5 + - - +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.4 35.3 - - + +
10B LYS* 3.7 8.5 + - + +
11B TYR* 3.9 27.4 - - + +
15B VAL* 3.8 18.2 - - + -
34B LEU* 4.1 33.2 - - + -
100B TRP* 4.0 11.9 - - + -
107B LEU* 3.8 5.5 - - + +
172B LEU* 3.0 37.0 + - + +
173B LEU* 3.7 12.6 - - + +
174B GLU 3.2 0.4 - - - -
175B LEU* 1.3 76.5 - - - +
177B GLY* 1.3 57.0 - - - +
178B PHE* 3.7 9.9 - - + -
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 4.5 5.2 - - - -
107B LEU* 4.2 14.6 - - - +
174B GLU 3.0 13.1 + - - -
175B LEU 3.2 1.4 - - - -
176B LEU* 1.3 78.8 - - - +
178B PHE* 1.3 66.5 + - - +
179B PRO* 3.3 10.1 - - - +
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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