Contacts of the helix formed by residues 157 - 170 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ASP* 3.1 22.2 - - - +
132C GLY* 3.9 11.0 - - - +
155C GLU* 2.9 11.7 + - - +
156C GLU* 1.3 75.5 - - - +
158C THR* 1.3 66.2 + - - +
159C THR 3.8 0.2 - - - +
160C GLY 3.3 15.4 + - - +
161C VAL* 3.0 26.2 + - - +
181C ASN* 3.5 8.1 - - - +
301C HIS* 4.3 4.3 - - + +
503C NAD 2.5 36.8 + - - +
603C AFX 3.3 24.9 + - - +
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Residues in contact with THR 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C THR* 1.3 78.2 + - - +
159C THR* 1.3 57.4 + - - +
161C VAL* 3.5 4.1 + - - +
162C HIS* 2.9 37.4 + - + +
181C ASN* 3.0 29.2 + - - +
182C ASP* 5.8 2.9 - - - +
191C ASN* 3.3 3.6 + - - -
503C NAD 2.6 58.2 + - - +
430D TYR* 6.3 0.7 - - + -
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Residues in contact with THR 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLY 4.3 3.8 - - - +
157C THR* 3.3 1.0 - - - -
158C THR* 1.3 78.4 - - - +
160C GLY* 1.3 64.2 + - - +
162C HIS* 3.1 9.6 + - + +
163C ASN* 3.0 22.1 + - + +
277C GLY* 4.3 12.2 + - - +
301C HIS* 4.0 9.5 - - + +
302C PHE* 3.6 37.1 + - + -
503C NAD 2.9 34.4 + - - -
416D TYR* 6.1 0.2 - - - +
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Residues in contact with GLY 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLY 3.6 19.9 + - - -
133C GLY* 4.2 0.8 - - - -
155C GLU* 3.3 27.6 - - - +
157C THR* 3.3 8.5 + - - +
159C THR* 1.3 79.5 - - - +
161C VAL* 1.3 55.4 + - - +
163C ASN* 3.1 8.5 + - - +
164C LEU* 3.0 28.6 + - - +
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C GLU* 3.4 26.0 - - + +
157C THR 3.0 18.1 + - - +
158C THR* 3.9 4.9 - - - +
160C GLY* 1.3 72.6 - - - +
162C HIS* 1.3 65.2 + - - +
164C LEU* 3.3 6.3 + - + +
165C TYR* 2.8 44.3 + - + -
179C ASN* 2.9 50.0 - - + +
181C ASN* 4.0 9.2 - - + -
182C ASP* 3.5 7.6 - - - +
383C VAL* 4.9 2.9 - - + -
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Residues in contact with HIS 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C THR* 2.9 20.5 + - + +
159C THR* 3.1 15.0 + - - +
161C VAL* 1.3 77.9 - - - +
163C ASN* 1.3 62.9 + - - +
165C TYR* 3.6 9.3 + - - +
166C LYS* 3.3 23.2 + - + +
503C NAD 6.1 0.7 - - - -
416D TYR 5.6 0.9 - - - -
417D LEU* 3.1 39.2 + - + +
418D GLY 5.5 0.4 - - - -
419D MET* 4.3 14.8 - - - +
427D PRO* 6.1 5.2 - - + -
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Residues in contact with ASN 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLY 4.9 3.6 - - - +
133C GLY* 4.3 9.3 + - - -
136C THR* 5.2 1.6 - - - -
137C ASN* 3.4 31.8 + - - +
159C THR* 3.0 12.6 + - + +
160C GLY* 3.1 13.8 + - - +
162C HIS* 1.3 74.7 - - - +
164C LEU* 1.3 70.7 + - - +
166C LYS* 3.1 20.1 + - - +
167C MET* 3.0 40.2 + - - +
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C GLY* 6.5 0.4 - - - -
136C THR* 4.1 28.7 - - + +
153C ILE* 4.8 3.8 - - + -
155C GLU* 3.6 33.4 - - + +
160C GLY 3.0 15.1 + - - +
161C VAL* 3.3 11.0 + - + +
163C ASN* 1.3 77.2 - - - +
165C TYR* 1.3 64.1 + - - +
167C MET* 2.9 12.8 + - - +
168C MET* 2.8 22.8 + - - +
173C LEU* 4.5 16.4 - - + +
177C ALA* 3.9 30.1 - - + -
178C ILE 5.3 1.8 - - - +
383C VAL* 4.8 19.7 - - + -
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Residues in contact with TYR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C VAL* 2.8 46.0 + - + -
162C HIS* 3.7 9.6 - - - +
163C ASN 3.4 0.2 - - - -
164C LEU* 1.3 78.2 - - - +
166C LYS* 1.3 56.5 + - - +
168C MET* 3.1 7.3 + - + +
169C ALA* 2.8 32.9 + - - +
179C ASN* 3.0 18.9 + - - -
182C ASP* 4.6 0.4 - - - -
383C VAL* 3.2 33.9 + - + +
385C PHE* 3.3 21.7 - + - -
427D PRO* 6.1 2.0 - - + -
429D HIS* 3.8 17.8 - + - -
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C HIS* 3.3 15.2 + - + +
163C ASN* 3.1 21.4 + - - +
165C TYR* 1.3 79.2 - - - +
167C MET* 1.3 63.6 + - + +
169C ALA* 3.5 5.5 + - - +
170C ASN* 3.2 43.4 + - - +
416D TYR 5.9 4.0 - - - +
418D GLY* 6.5 1.3 - - - -
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Residues in contact with MET 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C THR* 4.6 9.6 - - + -
137C ASN* 3.6 14.8 - - - +
140C HIS* 3.6 45.8 - - + +
163C ASN* 3.0 42.5 + - - +
164C LEU* 2.9 13.9 + - - +
166C LYS* 1.3 76.2 - - + +
168C MET* 1.3 58.4 + - - +
170C ASN 3.2 2.4 + - - -
171C GLY 2.8 7.6 + - - -
172C ILE* 2.6 55.3 + - + +
173C LEU* 3.8 13.5 - - + +
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Residues in contact with MET 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C LEU 2.8 11.6 + - - +
165C TYR* 3.6 12.1 - - + +
167C MET* 1.3 73.0 - - - +
169C ALA* 1.3 60.7 + - - +
171C GLY* 2.8 27.3 + - - -
173C LEU* 3.8 29.8 - - + +
381C VAL* 3.6 11.7 - - + +
382C GLY* 3.4 33.9 - - - -
383C VAL* 4.9 10.1 - - + +
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR 2.8 17.0 + - - +
166C LYS* 3.5 8.7 - - - +
168C MET* 1.3 79.2 - - - +
170C ASN* 1.3 64.5 + - - +
171C GLY 3.2 2.3 + - - -
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Residues in contact with ASN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LYS* 3.2 32.5 + - - +
169C ALA* 1.3 81.5 - - - +
171C GLY* 1.3 63.3 + - - +
172C ILE* 3.1 33.4 + - + +
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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