Contacts of the helix formed by residues 237 - 248 (chain A) in PDB entry 3N1Z
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 GLN 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A TYR* 2.9 34.7 + - - +
111A GLU* 3.2 18.9 - - - +
114A MET* 3.7 8.5 - - - +
123A ASN* 3.0 23.9 + - - +
126A MET* 4.0 16.4 - - + -
127A ALA* 3.1 37.5 - - - +
189A SER* 3.9 7.5 - - - -
193A THR* 3.7 7.4 - - + +
234A HIS* 2.8 30.0 - - - +
235A ALA 3.4 0.4 - - - -
236A GLN* 1.3 80.4 - - + +
238A GLY* 1.3 61.7 + - - +
240A PRO* 3.5 1.6 - - - +
241A SER* 3.5 12.8 + - - -
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Residues in contact with GLY 238 (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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189A SER* 2.7 30.3 - - - -
190A ILE* 4.5 0.4 - - - +
193A THR* 2.8 12.8 + - - -
194A PHE* 4.0 13.2 - - - -
235A ALA 3.9 0.6 + - - -
236A GLN 2.6 6.7 + - - -
237A GLN* 1.3 71.4 - - - +
239A GLY* 1.3 63.6 + - - -
241A SER* 2.9 13.9 + - - -
242A LEU* 3.0 16.3 + - - +
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Residues in contact with GLY 239 (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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194A PHE* 4.5 15.2 - - - +
235A ALA 5.1 0.4 + - - -
236A GLN 2.8 13.4 + - - -
238A GLY* 1.3 69.7 - - - -
240A PRO* 1.3 65.9 - - - +
241A SER 3.1 0.2 + - - -
242A LEU* 3.1 8.4 + - - +
243A LYS* 3.1 24.3 + - - +
309A LEU* 3.9 14.8 - - - +
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Residues in contact with PRO 240 (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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47A TYR* 3.2 35.8 - - + +
48A ASP 4.0 15.9 - - - +
49A GLU* 4.4 0.9 - - - -
50A PRO* 4.0 25.4 - - + -
236A GLN 3.2 14.6 - - - +
237A GLN 3.5 7.0 - - - +
239A GLY* 1.3 88.9 - - - +
241A SER* 1.3 58.3 + - - -
243A LYS* 3.4 15.7 - - + +
244A ILE* 3.2 28.8 + - - +
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Residues in contact with SER 241 (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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44A TRP* 4.4 13.8 - - - -
47A TYR* 3.6 11.6 - - - -
123A ASN* 4.0 6.4 + - - -
186A VAL* 4.7 11.8 - - - +
189A SER* 3.0 26.1 + - - -
190A ILE* 4.4 7.2 - - - -
237A GLN 3.5 7.6 + - - -
238A GLY* 2.9 11.0 + - - -
240A PRO* 1.3 77.1 - - - +
242A LEU* 1.3 64.8 + - - +
244A ILE* 3.3 3.8 + - - +
245A LEU* 3.1 28.5 + - - +
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Residues in contact with LEU 242 (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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190A ILE* 3.3 38.1 - - + -
194A PHE* 3.6 48.2 - - + -
238A GLY 3.0 13.8 + - - +
239A GLY 3.6 6.3 - - - +
241A SER* 1.3 75.0 - - - +
243A LYS* 1.3 58.4 + - - +
245A LEU* 3.3 3.7 + - - +
246A VAL* 2.9 36.3 + - - +
254A ALA* 3.8 18.6 - - + -
258A VAL* 3.9 10.8 - - + -
309A LEU* 4.1 16.4 - - + -
311A LEU* 4.1 14.6 - - + -
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A GLY 3.1 12.4 + - - +
240A PRO* 3.4 17.3 - - + +
242A LEU* 1.3 77.3 - - - +
244A ILE* 1.3 60.5 + - + +
246A VAL* 3.2 4.8 + - - +
247A GLU* 2.8 43.7 + - + +
308A ASP 5.5 3.5 + - - +
309A LEU* 4.1 27.8 - - + +
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Residues in contact with ILE 244 (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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39A ILE* 4.1 11.4 - - + -
43A ALA 3.9 10.8 - - - +
44A TRP* 3.5 48.2 - - + +
46A LYS* 4.8 2.5 - - + -
47A TYR* 3.7 38.6 - - + +
240A PRO 3.2 13.7 + - - +
241A SER 3.8 3.6 - - - +
243A LYS* 1.3 82.1 - - + +
245A LEU* 1.3 63.8 + - - +
247A GLU* 3.9 17.9 - - - +
248A ASN* 2.5 41.5 + - - +
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Residues in contact with LEU 245 (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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37A ARG* 4.5 17.5 - - + +
39A ILE* 3.5 24.7 - - + -
44A TRP* 4.1 14.8 - - + -
186A VAL* 3.8 22.9 - - + -
190A ILE* 3.9 20.0 - - + -
241A SER 3.1 17.0 + - - +
242A LEU 3.6 4.0 - - - +
244A ILE* 1.3 77.0 - - - +
246A VAL* 1.3 56.0 + - - +
248A ASN* 2.9 20.4 + - - +
250A LYS* 2.6 44.2 + - + +
253A GLU* 5.5 0.4 - - + -
254A ALA* 4.1 15.7 - - + +
257A MET* 5.4 1.6 - - - -
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Residues in contact with VAL 246 (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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242A LEU 2.9 22.9 + - - +
243A LYS* 3.9 3.1 - - - +
245A LEU* 1.3 71.9 - - - +
247A GLU* 1.3 60.3 + - - +
248A ASN 2.8 18.7 - - - +
250A LYS 3.9 2.0 - - - -
251A LYS* 4.2 33.7 - - + +
254A ALA* 4.6 3.8 - - + -
309A LEU 4.1 19.7 - - - +
310A GLY* 4.7 3.8 - - - +
311A LEU* 3.5 32.1 - - + -
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Residues in contact with GLU 247 (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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43A ALA 4.7 1.9 - - - +
46A LYS* 4.3 17.3 - - - +
243A LYS* 2.8 30.3 + - + +
244A ILE* 3.8 22.3 - - - +
246A VAL* 1.3 73.2 - - - +
248A ASN* 1.3 72.8 + - - +
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Residues in contact with ASN 248 (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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39A ILE* 3.4 36.8 - - + +
43A ALA* 4.3 11.4 - - - +
244A ILE* 2.5 36.6 + - - +
245A LEU 2.9 3.1 - - - +
246A VAL 2.8 15.9 - - - +
247A GLU* 1.3 90.7 + - - +
249A GLY* 1.3 70.0 + - - +
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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