Contacts of the helix formed by residues 157 - 170 (chain D) in PDB entry 3NJ4
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 157 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D ASP* 3.2 21.1 - - - +
132D GLY* 3.7 8.7 - - - +
155D GLU* 3.3 8.3 + - - +
156D GLU* 1.3 78.0 - - - +
158D THR* 1.3 61.4 + - - +
160D GLY 3.3 16.6 + - - +
161D VAL* 3.0 30.8 + - - +
181D ASN* 3.2 9.4 - - - +
301D HIS* 4.1 4.3 - - + +
504D NAD 2.6 37.5 + - - +
604D AFX 3.3 21.2 + - - +
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Residues in contact with THR 158 (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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430C TYR* 6.3 0.2 - - + -
157D THR* 1.3 77.9 + - - +
159D THR* 1.3 57.3 + - - +
161D VAL* 3.3 6.1 + - + +
162D HIS* 2.9 34.2 + - + +
181D ASN* 2.8 27.7 + - - +
182D ASP* 5.9 0.4 - - - +
191D ASN* 3.5 2.3 + - - -
504D NAD 2.6 60.0 + - - +
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Residues in contact with THR 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D GLY 4.2 3.4 - - - +
157D THR* 4.3 0.7 - - - -
158D THR* 1.3 78.0 - - - +
160D GLY* 1.3 64.2 - - - +
162D HIS* 3.2 10.2 + - - +
163D ASN* 3.2 19.8 + - + +
277D GLY* 4.6 10.8 + - - +
301D HIS* 3.9 8.7 - - + +
302D PHE* 3.6 39.7 + - + -
504D NAD 2.8 35.9 + - - -
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Residues in contact with GLY 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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132D GLY 3.3 20.4 - - - -
133D GLY* 4.0 2.5 - - - -
155D GLU* 3.3 26.4 - - - +
157D THR* 3.3 8.3 + - - +
158D THR 3.3 0.4 - - - -
159D THR* 1.3 79.6 - - - +
161D VAL* 1.3 61.4 + - - +
163D ASN* 3.2 15.1 + - - +
164D LEU* 3.2 16.1 + - - +
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Residues in contact with VAL 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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155D GLU* 3.5 27.8 - - + +
157D THR 3.0 16.1 + - - +
158D THR* 3.8 6.5 - - + +
160D GLY* 1.3 72.1 - - - +
162D HIS* 1.3 67.3 + - - +
163D ASN 3.0 1.8 - - - -
164D LEU* 3.2 17.3 + - + +
165D TYR* 3.1 29.9 + - + -
179D ASN* 2.9 52.5 - - + +
181D ASN* 4.3 2.7 - - + -
182D ASP* 3.8 7.2 - - - +
383D VAL* 5.4 0.4 - - + -
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Residues in contact with HIS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C TYR 5.2 1.6 - - - -
417C LEU* 3.1 44.2 + - + +
419C MET* 4.3 13.6 - - + +
158D THR* 2.9 20.3 + - + +
159D THR* 3.2 14.8 - - - +
161D VAL* 1.3 78.3 - - - +
163D ASN* 1.3 62.9 + - - +
165D TYR* 3.7 7.4 + - - +
166D LYS* 3.3 25.9 + - + +
277D GLY 6.1 0.2 - - - -
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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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132D GLY 5.2 2.5 - - - +
133D GLY* 4.4 4.9 + - - -
136D THR* 4.3 6.1 + - - -
137D ASN* 2.9 38.9 + - - +
159D THR* 3.2 7.7 + - + +
160D GLY* 3.3 12.8 + - - +
161D VAL 3.0 0.6 - - - -
162D HIS* 1.3 79.2 - - - +
164D LEU* 1.3 67.8 + - - +
166D LYS* 3.1 17.5 + - - +
167D MET* 2.9 46.5 + - - +
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Residues in contact with LEU 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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133D GLY* 6.5 0.9 - - - -
136D THR* 4.8 22.0 - - + +
153D ILE* 5.0 4.7 - - + -
155D GLU* 3.6 30.1 - - + +
160D GLY 3.2 9.8 + - - +
161D VAL* 3.2 15.8 + - + +
163D ASN* 1.3 78.3 - - - +
165D TYR* 1.3 64.2 + - - +
167D MET* 3.0 13.8 + - - +
168D MET* 2.9 23.3 + - - +
173D LEU* 4.5 21.1 - - + +
177D ALA* 3.9 29.8 - - + -
178D ILE 5.2 2.5 - - - +
179D ASN* 5.4 0.2 - - - -
383D VAL* 4.5 19.3 - - + -
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Residues in contact with TYR 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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427C PRO* 6.0 3.1 - - + -
429C HIS* 3.8 18.9 - + - -
161D VAL* 3.1 43.1 + - + -
162D HIS* 4.0 8.1 - - - +
164D LEU* 1.3 77.7 - - - +
166D LYS* 1.3 53.9 + - - +
168D MET* 3.2 3.5 + - + +
169D ALA* 2.7 38.3 + - - +
179D ASN* 3.0 17.3 + - - -
383D VAL* 3.3 42.1 - - + +
385D PHE* 3.3 25.5 - + - -
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Residues in contact with LYS 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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415C GLN 4.9 6.5 + - - -
416C TYR* 4.5 13.1 + - - +
417C LEU 6.1 0.2 - - - -
418C GLY* 5.8 4.4 - - - +
162D HIS* 3.3 19.4 + - + +
163D ASN* 3.1 21.2 + - - +
165D TYR* 1.3 79.9 - - - +
167D MET* 1.3 59.6 + - + +
169D ALA* 3.3 3.4 + - - +
170D ASN* 2.7 51.1 + - - +
172D ILE* 6.0 2.2 - - + -
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Residues in contact with MET 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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136D THR* 4.6 7.0 - - - -
137D ASN* 3.4 19.7 - - - +
140D HIS* 4.2 26.9 - - + -
141D THR* 5.4 5.2 - - + -
163D ASN* 2.9 42.8 + - - +
164D LEU* 3.0 13.9 + - - +
166D LYS* 1.3 78.2 - - + +
168D MET* 1.3 55.5 + - - +
170D ASN 3.3 0.5 + - - -
171D GLY 2.8 7.8 + - - -
172D ILE* 2.6 66.5 + - + -
173D LEU* 3.2 21.5 + - + +
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Residues in contact with MET 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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164D LEU 2.9 14.1 + - - +
165D TYR* 3.7 7.9 - - + +
167D MET* 1.3 77.5 - - - +
169D ALA* 1.3 63.5 + - - +
171D GLY* 3.2 17.3 + - - -
173D LEU* 3.8 26.6 - - + +
381D VAL* 3.6 14.1 - - + +
382D GLY* 3.4 32.3 - - - -
383D VAL* 4.5 11.4 - - + -
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Residues in contact with ALA 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 TYR 2.7 21.8 + - - +
166D LYS* 3.7 6.3 - - - +
168D MET* 1.3 73.9 - - - +
170D ASN* 1.3 64.7 + - - +
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Residues in contact with ASN 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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166D LYS* 2.7 38.8 + - - +
169D ALA* 1.3 83.1 - - - +
171D GLY* 1.3 61.5 + - - +
172D ILE* 3.6 26.4 + - + +
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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