Contacts of the helix formed by residues 159 - 169 (chain D) in PDB entry 6N0M
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 LEU 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D ILE* 3.8 26.5 - - + -
118D MET* 4.2 8.7 - - + -
155D LYS 4.0 0.2 + - - -
156D LEU* 3.3 16.8 + - + +
157D ARG 3.1 0.6 - - - -
158D LYS* 1.3 76.5 - - - +
160D SER* 1.3 57.5 + - - +
161D GLU 3.2 0.8 + - - -
162D ILE* 3.5 8.7 - - + +
163D ASN* 2.8 30.6 + - + +
181D LEU* 3.9 20.9 - - + -
189D TRP* 3.4 50.5 - - + +
194D LEU* 4.3 9.4 - - + -
197D ALA* 4.1 7.6 - - + -
201D LEU* 4.1 19.7 - - + -
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Residues in contact with SER 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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118D MET* 3.3 10.1 - - - +
122D ARG* 5.1 1.7 + - - -
149D LEU* 3.2 28.3 - - - +
157D ARG 2.9 18.1 + - - -
158D LYS 3.1 0.2 - - - -
159D LEU* 1.3 77.8 - - - +
161D GLU* 1.3 60.5 + - - +
163D ASN* 3.9 8.1 - - - +
164D LYS* 3.3 23.4 + - - +
315D PHE 4.8 0.5 + - - -
316D VAL* 5.2 0.8 - - - -
317D GLU* 3.7 33.5 + - - +
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Residues in contact with GLU 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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158D LYS 3.6 8.2 + - - +
159D LEU 3.2 0.8 - - - -
160D SER* 1.3 74.5 - - - +
162D ILE* 1.3 66.7 + - - +
164D LYS* 3.1 36.5 + - - +
165D LEU* 3.0 32.4 + - + +
177D HIS* 3.6 35.9 + - + +
181D LEU* 6.4 0.4 - - + -
317D GLU* 5.5 0.2 + - - -
321D PHE* 5.8 0.2 - - - -
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Residues in contact with ILE 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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158D LYS 4.7 1.0 + - - -
159D LEU* 3.5 15.2 - - + +
161D GLU* 1.3 78.9 - - - +
163D ASN* 1.3 64.7 + - - +
165D LEU* 4.4 7.9 - - - -
166D LEU* 3.0 35.8 + - + +
173D ILE* 3.8 31.2 - - + -
177D HIS* 4.9 12.7 - - + +
178D ILE* 3.8 28.7 - - + -
181D LEU* 4.1 27.1 - - + +
198D LEU* 3.9 27.1 - - + -
201D LEU* 4.6 6.7 - - + -
471D ALA* 5.0 0.9 - - + -
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Residues in contact with ASN 163 (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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118D MET* 3.1 44.1 + - - +
119D ALA 3.5 1.0 - - - +
122D ARG* 3.3 11.5 - - - +
159D LEU* 2.8 20.8 + - + +
160D SER* 3.9 7.2 - - - +
162D ILE* 1.3 78.4 - - - +
164D LYS* 1.3 64.6 - - - +
165D LEU 3.1 0.5 + - - -
166D LEU* 3.2 3.2 + - - +
167D ALA* 3.0 21.0 + - - +
201D LEU* 3.2 24.3 - - + +
205D HIS* 2.7 34.5 + - - -
315D PHE 5.6 1.0 + - - -
316D VAL* 5.7 0.6 - - - +
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Residues in contact with LYS 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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122D ARG* 3.7 31.4 - - - +
160D SER 3.3 14.0 + - - +
161D GLU* 3.1 36.6 + - - +
163D ASN* 1.3 78.0 - - - +
165D LEU* 1.3 63.0 + - - +
168D HIS* 3.2 26.0 + - - +
317D GLU 3.9 16.4 - - - +
318D ASP* 3.9 14.0 + - + +
321D PHE* 3.3 56.8 - - + -
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Residues in contact with LEU 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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161D GLU* 3.0 27.4 + - + +
162D ILE* 3.9 2.9 - - - +
164D LYS* 1.3 79.4 - - - +
166D LEU* 1.3 64.2 + - - +
168D HIS 3.0 0.9 + - - -
169D ARG 2.7 35.3 + - - +
170D PRO* 3.0 7.6 - - - -
172D LEU* 4.0 25.8 - - + +
173D ILE* 3.8 23.1 - - + +
177D HIS* 3.4 43.3 - - + +
321D PHE* 4.0 26.7 - - + -
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Residues in contact with LEU 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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162D ILE* 3.0 38.6 + - + +
163D ASN 3.5 3.1 - - - +
165D LEU* 1.3 76.1 - - - +
167D ALA* 1.3 65.6 + - - +
170D PRO* 4.0 10.0 - - - +
173D ILE* 3.5 21.0 - - + +
198D LEU* 4.0 20.9 - - + +
201D LEU* 4.2 20.0 - - + -
202D THR* 3.8 13.7 - - + -
205D HIS* 3.7 14.3 + - + +
401D PHE* 5.1 1.2 - - - -
463D ARG* 4.6 2.4 + - - -
467D ALA* 3.7 47.6 - - + +
471D ALA* 4.0 7.9 - - + -
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Residues in contact with ALA 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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122D ARG* 3.9 5.8 - - + -
123D HIS* 3.9 8.1 - - - +
163D ASN 3.0 11.0 + - - +
166D LEU* 1.3 79.5 - - - +
168D HIS* 1.3 84.5 - - + +
205D HIS* 3.4 30.8 - - + +
401D PHE* 4.3 8.0 - - - -
430D CYS* 6.0 0.7 - - - -
463D ARG* 2.5 30.4 + - - +
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Residues in contact with HIS 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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122D ARG* 3.4 51.4 + - - +
123D HIS* 3.9 20.7 - + - -
164D LYS* 3.2 22.6 + - + +
165D LEU 3.0 2.0 + - - -
167D ALA* 1.3 88.8 - - + +
169D ARG* 1.3 67.5 + - - +
170D PRO* 3.9 3.6 - - - +
171D TRP* 4.1 0.5 - - - -
321D PHE* 3.5 26.5 + - + -
322D GLY* 3.6 26.1 - - - +
323D TYR* 3.4 29.3 + - - +
401D PHE* 5.0 1.5 - - - -
430D CYS* 4.4 6.5 + - - +
431D TYR* 6.0 0.4 - + - -
433D GLU* 4.1 9.9 - - - -
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Residues in contact with ARG 169 (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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165D LEU* 2.7 18.9 + - + +
168D HIS* 1.3 83.4 - - - +
170D PRO* 1.3 68.9 - - - +
171D TRP* 3.0 36.0 + - + +
172D LEU* 3.0 38.2 + - + +
321D PHE* 3.1 45.6 - - + +
322D GLY 3.3 10.2 + - - +
323D TYR 2.9 19.9 + - - +
324D GLU 3.2 22.6 + - - -
325D ASP* 3.6 29.3 + - - +
332D GLN* 3.9 8.1 - - - +
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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