Contacts of the helix formed by residues 157 - 170 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ASP* 3.4 22.7 - - - +
132A GLY* 3.7 13.2 - - - +
155A GLU* 3.2 3.3 + - - +
156A GLU* 1.3 78.9 - - - +
158A THR* 1.3 66.0 + - - +
159A THR* 3.7 1.6 - - - +
160A GLY 3.1 18.4 + - - +
161A VAL* 3.0 21.5 + - - +
181A ASN* 3.2 8.3 - - - +
301A HIS* 4.0 3.4 - - - +
501A NAD 2.6 32.3 + - - +
601A AFX 3.0 27.4 + - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 1.3 72.8 + - - +
159A THR* 1.3 65.7 + - - +
161A VAL* 3.2 6.3 + - + +
162A HIS* 2.8 40.3 + - + +
181A ASN* 2.7 32.9 + - - +
182A ASP* 5.4 5.2 - - - +
191A ASN* 3.4 3.3 + - - -
501A NAD 2.5 53.9 + - - +
430B TYR* 6.4 0.2 - - + -
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 4.2 2.5 - - - +
157A THR* 3.3 1.9 - - - -
158A THR* 1.3 77.6 - - - +
160A GLY* 1.3 64.5 + - - +
162A HIS* 3.0 18.8 + - + +
163A ASN* 3.1 12.4 + - + +
277A GLY* 4.5 9.3 + - - +
301A HIS* 3.7 12.5 - - + +
302A PHE* 3.4 39.2 + - + -
501A NAD 3.0 36.2 + - - -
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Residues in contact with GLY 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY* 3.7 18.6 - - - -
133A GLY* 4.1 0.8 - - - -
155A GLU* 3.2 27.9 - - - +
157A THR* 3.1 8.7 + - - +
159A THR* 1.3 76.9 - - - +
161A VAL* 1.3 55.4 + - - +
163A ASN* 2.6 29.7 + - - +
164A LEU* 3.0 9.5 + - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 3.2 27.4 - - + +
157A THR 3.0 13.2 + - - +
158A THR* 3.5 12.6 - - + +
160A GLY* 1.3 72.6 - - - +
162A HIS* 1.3 66.1 + - + +
164A LEU* 3.1 17.0 + - + +
165A TYR* 3.2 24.8 + - + -
179A ASN* 2.8 51.6 - - - +
181A ASN* 3.7 12.6 - - + +
182A ASP* 3.5 9.0 - - - +
383A VAL* 5.6 0.9 - - + -
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Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 2.8 34.3 + - + +
159A THR* 3.1 16.6 - - - +
161A VAL* 1.3 78.1 - - + +
163A ASN* 1.3 60.0 + - - +
165A TYR* 3.5 11.5 + + - +
166A LYS* 3.2 21.7 + - - +
501A NAD 5.1 5.4 + - - -
417B LEU* 4.8 16.9 + - + -
419B MET* 6.3 3.1 - - - -
425B PHE 6.2 0.2 - - - -
427B PRO* 5.0 17.9 - - + +
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Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY 5.1 3.4 - - - +
133A GLY* 4.6 2.8 + - - -
136A THR* 4.3 4.6 + - - -
137A ASN* 3.2 35.0 + - - +
159A THR* 3.1 10.0 + - + +
160A GLY* 2.6 22.0 + - - +
162A HIS* 1.3 69.8 - - - +
164A LEU* 1.3 56.4 + - - -
166A LYS* 3.2 28.0 + - - +
167A MET* 2.8 61.7 + - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 4.9 4.5 - - + +
153A ILE* 4.4 12.8 - - + -
155A GLU* 3.7 32.5 - - + +
160A GLY 3.0 12.5 + - - +
161A VAL* 3.1 10.7 + - + +
163A ASN* 1.3 75.6 - - - +
165A TYR* 1.3 57.3 + - - +
167A MET* 3.3 24.2 + - + +
168A MET* 2.9 30.2 + - - +
173A LEU* 4.0 15.1 - - + +
177A ALA* 3.6 32.1 - - + -
178A ILE 4.6 5.2 - - - +
383A VAL* 4.5 23.8 - - + +
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 3.2 41.3 + - + -
162A HIS* 3.8 11.4 - + - +
163A ASN 3.2 0.6 - - - -
164A LEU* 1.3 72.9 - - - +
166A LYS* 1.3 58.1 + - - +
167A MET 3.0 1.1 - - - -
168A MET* 3.8 3.7 - - + +
169A ALA* 2.7 38.3 + - - +
179A ASN* 2.8 20.1 + - - -
383A VAL* 3.3 37.3 + - + +
385A PHE* 3.4 23.0 - + - -
427B PRO* 5.7 2.9 - - + -
429B HIS* 3.4 20.1 - + - -
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A HIS 3.2 10.3 + - - +
163A ASN* 3.2 28.6 + - - +
165A TYR* 1.3 78.4 - - - +
167A MET* 1.3 61.7 + - - +
169A ALA* 3.8 6.6 - - - +
170A ASN* 2.6 48.4 + - - +
416B TYR 5.6 5.8 - - - +
417B LEU 6.5 0.4 - - - -
418B GLY* 5.9 7.0 - - - -
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 4.2 11.4 - - - +
137A ASN* 4.0 11.7 - - - +
140A HIS* 5.0 16.2 - - - -
163A ASN* 2.8 48.0 + - - +
164A LEU* 3.4 38.4 - - + +
166A LYS* 1.3 80.6 - - - +
168A MET* 1.3 61.9 + - - +
169A ALA 3.1 1.1 - - - -
170A ASN* 2.8 21.2 + - - +
171A GLY 2.9 9.0 + - - -
172A ILE* 3.1 19.1 + - + +
173A LEU* 3.9 24.9 - - + +
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Residues in contact with MET 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU 2.9 21.2 + - - +
165A TYR* 3.9 5.4 - - + +
167A MET* 1.3 72.6 - - - +
169A ALA* 1.3 59.4 + - - +
171A GLY* 2.8 29.8 + - - -
173A LEU* 3.7 26.1 - - + +
381A VAL* 3.5 14.4 - - + +
382A GLY* 3.4 32.5 - - - -
383A VAL* 4.6 10.5 - - + +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TYR 2.7 22.9 + - - +
166A LYS* 3.8 8.5 - - - +
168A MET* 1.3 75.4 - - - +
170A ASN* 1.3 59.9 + - - +
171A GLY 3.4 0.9 + - - -
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Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 2.6 38.6 + - - +
167A MET* 2.8 7.5 + - - +
169A ALA* 1.3 77.7 - - - +
171A GLY* 1.3 64.1 + - - +
172A ILE* 3.2 31.2 + - + +
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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