Contacts of the helix formed by residues 159 - 173 (chain D) in PDB entry 5B6N
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 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C TYR* 2.8 23.0 + - - +
156C ASN* 3.3 22.9 + - + +
159C GLU* 4.1 26.4 - - + +
156D ASN* 2.4 35.6 + - + +
158D ASP* 1.3 71.6 - - - +
160D ILE* 1.3 67.6 + - + +
161D LEU 3.2 0.2 - - - -
162D ARG* 2.3 55.1 + - - +
163D VAL* 3.0 28.4 + - - +
182D LYS* 5.0 0.7 + - - -
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ILE* 4.4 25.1 - - + -
37D PHE* 5.9 0.4 - - + -
61D PHE* 4.4 13.7 - - + -
134D VAL* 3.8 36.8 - - + -
136D VAL* 5.0 6.7 - - + -
145D LEU* 6.4 1.3 - - + -
147D ILE* 5.3 8.1 - - + -
155D ARG* 4.5 2.7 - - - -
156D ASN 3.6 19.1 - - - +
157D PHE* 3.6 34.2 + - + +
159D GLU* 1.3 77.4 - - + +
161D LEU* 1.3 61.5 + - - +
163D VAL* 3.3 9.7 - - - +
164D VAL* 3.0 23.7 + - + +
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 5.8 7.4 - - + -
60D GLU* 4.6 24.9 - - + +
61D PHE* 3.9 37.6 - - + -
64D ARG* 4.8 11.7 - - - +
157D PHE 3.2 14.6 + - - +
158D ASP* 4.5 12.8 - - + +
159D GLU 3.2 0.2 - - - -
160D ILE* 1.3 80.2 - - - +
162D ARG* 1.3 63.4 + - - +
164D VAL* 3.3 17.0 - - + +
165D ILE* 3.2 35.5 - - + +
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Residues in contact with ARG 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C TYR* 3.8 2.2 - - - -
153C THR* 5.3 1.6 - - - +
154C GLY 3.7 17.2 + - - -
156C ASN* 3.7 23.2 - - - +
158D ASP 3.4 18.3 + - - +
159D GLU* 2.3 46.1 + - - +
161D LEU* 1.3 81.4 - - - +
163D VAL* 1.3 77.5 + - - +
165D ILE* 3.4 23.9 - - - +
166D SER* 3.4 7.6 + - - -
177D THR* 5.2 1.4 + - - -
180D ASP 4.3 3.0 - - - +
181D TRP* 3.0 57.3 + - + +
182D LYS* 3.7 26.5 - - - +
183D ASP 5.6 1.1 - - - +
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Residues in contact with VAL 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C TYR* 3.4 21.5 - - + +
153C THR* 3.8 9.4 - - + -
136D VAL* 5.6 2.5 - - + -
145D LEU* 3.7 30.7 - - + -
159D GLU* 3.0 12.7 + - - +
160D ILE* 3.3 17.9 - - + +
162D ARG* 1.3 104.2 - - - +
164D VAL* 1.3 57.2 + - + +
165D ILE 3.0 5.4 - - - -
166D SER* 3.2 6.5 + - - -
167D LEU* 2.6 43.0 + - + +
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Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TRP* 4.3 8.3 - - + -
35D ILE* 3.9 27.6 - - + -
61D PHE* 4.1 16.4 - - + -
64D ARG* 5.6 4.3 - - + -
66D VAL* 4.1 14.8 - - + -
136D VAL* 4.2 19.5 - - + -
160D ILE* 3.0 17.6 + - + +
161D LEU* 3.3 24.7 - - + +
163D VAL* 1.3 77.0 - - + +
165D ILE* 1.3 60.9 + - + +
167D LEU* 3.8 8.3 - - + +
168D GLN* 3.2 30.9 + - - +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ARG* 4.1 28.5 - - + +
161D LEU* 3.2 31.0 - - + +
162D ARG* 3.4 11.7 - - - +
164D VAL* 1.3 81.5 - - + +
166D SER* 1.3 55.0 + - - +
168D GLN* 3.0 10.5 + - - +
169D LEU* 2.8 38.5 + - + +
181D TRP* 4.4 12.8 - - + -
183D ASP* 3.4 41.1 - - + +
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C THR* 2.3 41.8 + - - +
162D ARG* 3.4 9.2 + - - -
163D VAL* 3.2 6.2 + - - -
165D ILE* 1.3 79.3 - - - +
167D LEU* 1.3 52.4 - - - +
169D LEU* 4.2 6.7 - - - -
170D THR* 2.2 42.6 + - - +
177D THR* 3.4 26.9 - - - +
181D TRP* 4.1 10.7 - - - -
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C PRO* 3.7 20.4 - - + -
152C THR* 5.4 1.1 - - - +
153C THR* 3.8 6.3 - - - +
33D TRP* 3.5 23.7 - - + -
136D VAL* 3.8 28.9 - - + -
144D LYS* 3.7 28.5 - - + +
145D LEU* 4.0 23.3 - - + -
163D VAL* 2.6 28.4 + - + +
164D VAL* 3.8 11.7 - - - +
166D SER* 1.3 72.8 - - - +
168D GLN* 1.3 60.5 + - - +
170D THR* 3.4 9.7 + - - +
171D ALA* 4.2 9.5 + - - +
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Residues in contact with GLN 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TRP* 3.4 38.7 - - + +
64D ARG* 3.3 42.2 - - - +
65D ASN 4.5 2.0 - - - +
66D VAL* 3.6 20.8 - - - +
164D VAL* 3.2 15.7 + - - +
165D ILE* 3.0 9.4 + - - +
167D LEU* 1.3 77.9 - - - +
169D LEU* 1.3 65.4 + - - +
170D THR 3.2 0.9 + - - -
171D ALA* 3.4 4.9 + - - +
172D GLU* 3.3 22.8 + - - +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ILE* 2.8 25.2 + - + +
166D SER* 3.8 3.4 - - - +
168D GLN* 1.3 74.5 - - - +
170D THR* 1.3 61.2 + - - +
171D ALA 3.2 0.4 - - - -
172D GLU* 4.0 6.7 - - + -
173D LYS* 3.2 32.4 + - + +
175D VAL* 3.8 25.5 - - + +
177D THR* 4.7 5.8 - - + -
181D TRP* 4.2 25.8 - - + -
187D VAL* 4.3 6.7 - - + -
223D GLN* 4.2 28.9 - - + +
224D PRO* 5.2 9.4 - - + +
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Residues in contact with THR 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C THR* 3.7 40.3 + - - +
153C THR* 4.0 2.4 + - - -
166D SER* 2.2 49.1 + - - +
167D LEU* 3.4 11.3 + - - +
168D GLN 3.2 0.2 - - - -
169D LEU* 1.3 72.3 - - - +
171D ALA* 1.3 56.5 + - - +
173D LYS 3.0 11.8 - - - +
174D ARG* 4.5 3.8 - - - +
175D VAL* 3.1 29.8 + - + +
177D THR* 3.7 13.5 - - + -
190D LEU* 6.0 0.2 - - - +
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Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TRP* 6.3 0.9 - - + -
167D LEU 4.4 8.3 - - - +
168D GLN 3.4 5.9 + - - +
170D THR* 1.3 80.7 + - - +
172D GLU* 1.3 66.8 + - - +
173D LYS 3.2 6.6 + - - +
174D ARG* 5.2 3.1 - - - +
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Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D GLN 3.3 15.4 + - - +
169D LEU* 4.2 7.0 - - + +
171D ALA* 1.3 78.6 - - - +
173D LYS* 1.3 99.0 + - + +
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Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU* 3.2 18.9 + - + +
170D THR 3.0 21.0 - - - +
171D ALA 3.9 4.0 - - - -
172D GLU* 1.3 115.9 + - + +
174D ARG* 1.3 59.6 + - - +
175D VAL* 2.9 22.5 + - + -
201D LEU* 5.5 8.1 - - + -
202D PHE* 5.5 3.4 - - + -
224D PRO* 3.9 35.9 - - + +
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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