Contacts of the helix formed by residues 232 - 251 (chain A) in PDB entry 4KNF
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 LYS 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A MET* 4.2 13.9 - - + -
47A PHE* 4.3 1.0 - - - -
65A SER* 5.5 0.3 - - - +
68A ILE* 3.5 28.0 - - + -
69A THR* 4.2 9.7 - - + +
72A ALA* 3.9 21.5 - - + -
97A ASN* 4.5 3.6 - - - +
98A TRP* 4.0 3.4 - - - -
101A THR* 3.1 21.4 + - - -
105A LEU* 5.4 2.2 - - + -
228A ASP* 2.8 39.7 + - + +
231A ASN* 1.3 72.7 - - - +
233A ILE* 1.3 67.6 + - - +
235A PHE* 5.5 0.2 - - - -
236A GLY* 3.2 17.3 + - - -
301A RET 1.3 73.6 - - + +
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Residues in contact with ILE 233 (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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36A VAL* 4.7 1.6 - - + +
39A GLY* 3.4 30.5 - - - +
40A MET* 3.5 32.1 - - + +
43A ALA* 4.1 17.5 - - + -
47A PHE* 3.7 3.8 - - - -
69A THR* 4.6 4.0 - - - -
229A PHE* 3.3 50.2 + - + +
232A LYS* 1.3 77.8 - - - +
234A LEU* 1.3 66.0 + - + +
236A GLY* 3.6 0.5 - - - -
237A LEU* 3.0 37.5 + - + +
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Residues in contact with LEU 234 (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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229A PHE* 3.1 38.8 + - + +
230A VAL* 3.1 37.2 + - + +
233A ILE* 1.3 77.6 - - + +
235A PHE* 1.3 62.5 + - - +
237A LEU* 3.1 23.5 + - + +
238A ILE* 3.1 26.4 + - + +
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Residues in contact with PHE 235 (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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105A LEU* 3.7 28.3 - - + -
108A GLU* 4.4 7.4 - - - -
109A PHE* 3.9 22.7 - + - -
112A ILE* 5.0 4.3 - - + -
188A ALA* 3.7 34.3 - - + -
189A MET* 4.5 4.5 - - + -
192A ILE* 3.9 31.6 - - + +
230A VAL 3.0 10.4 + - - +
231A ASN 3.2 23.8 - - - +
232A LYS 4.1 0.4 + - - -
233A ILE 3.4 0.2 - - - -
234A LEU* 1.3 76.1 - - - +
236A GLY* 1.3 64.4 + - - +
238A ILE* 3.1 29.0 + - + +
239A ILE* 3.2 35.5 + - + +
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Residues in contact with GLY 236 (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 PHE* 3.5 17.9 - - - -
65A SER* 4.2 15.2 + - - -
108A GLU* 6.5 0.2 - - - -
232A LYS 3.2 18.3 + - - -
233A ILE 3.6 4.0 - - - -
235A PHE* 1.3 80.3 - - - +
237A LEU* 1.3 56.0 + - - +
239A ILE* 3.1 7.6 + - - +
240A TRP* 2.9 27.2 + - - +
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Residues in contact with LEU 237 (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* 6.3 1.1 - - + -
46A PHE* 3.8 35.4 - - + -
47A PHE* 3.7 10.2 - - + -
233A ILE* 3.0 34.0 + - + +
234A LEU* 3.1 23.1 + - + +
236A GLY* 1.3 74.2 - - - +
238A ILE* 1.3 57.3 + - - +
240A TRP* 3.4 12.9 + - + +
241A ASN* 2.8 30.3 + - - +
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Residues in contact with ILE 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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188A ALA* 3.7 28.7 - - + +
192A ILE* 5.4 5.8 - - + -
234A LEU* 3.1 15.8 + - + +
235A PHE* 3.1 25.4 + - + +
237A LEU* 1.3 75.4 - - + +
239A ILE* 1.3 64.4 + - + +
241A ASN* 3.2 6.6 + - - +
242A VAL* 3.0 32.3 + - + +
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Residues in contact with ILE 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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58A TRP* 4.5 12.8 - - + -
61A SER* 4.1 18.6 - - - -
62A LEU* 4.5 9.0 - - + -
65A SER* 4.9 2.5 - - - +
108A GLU* 4.0 24.9 - - - +
112A ILE* 4.5 9.9 - - + -
185A ALA* 4.3 27.4 - - + -
188A ALA* 4.6 4.5 - - + -
235A PHE* 3.2 39.9 + - + +
236A GLY* 3.1 10.1 + - - +
238A ILE* 1.3 74.5 - - + +
240A TRP* 1.3 66.5 + - - +
242A VAL* 3.5 4.6 + - + +
243A ALA* 3.0 21.8 + - - +
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Residues in contact with TRP 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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46A PHE* 3.5 33.1 - + - -
47A PHE* 4.6 9.9 - + + -
50A GLU* 2.8 45.7 + - + +
54A VAL* 5.1 0.2 - - + -
62A LEU* 4.2 21.0 - - + +
236A GLY 2.9 13.5 + - - +
237A LEU* 3.5 21.1 - - + +
239A ILE* 1.3 76.5 - - - +
241A ASN* 1.3 92.0 + - + +
243A ALA* 3.3 5.3 + - - +
244A VAL* 2.9 54.1 + - + +
60B THR* 3.6 20.9 - - + -
111B LEU* 5.0 10.8 - - + -
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Residues in contact with ASN 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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237A LEU 2.8 21.3 + - - +
238A ILE* 3.2 7.6 + - + +
240A TRP* 1.3 92.9 - - + +
242A VAL* 1.3 66.5 + - + +
244A VAL* 4.0 3.3 - - - +
245A LYS* 3.2 48.5 + - - +
110B TYR* 5.5 3.7 + - - -
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Residues in contact with VAL 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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58A TRP* 3.9 19.3 - - + -
181A ALA* 3.6 32.4 - - + +
184A SER* 3.7 26.2 - - - +
185A ALA* 4.5 6.3 - - + +
238A ILE* 3.0 27.2 + - + +
239A ILE* 3.9 5.2 - - + +
241A ASN* 1.3 77.8 - - + +
243A ALA* 1.3 58.2 + - - +
245A LYS* 3.7 17.1 - - - +
246A GLU* 3.0 27.9 + - - +
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Residues in contact with ALA 243 (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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54A VAL* 3.8 11.7 - - + -
58A TRP* 3.4 45.8 - - + -
62A LEU* 4.5 3.8 - - + -
239A ILE 3.0 20.0 + - - +
240A TRP* 3.7 4.5 - - - +
242A VAL* 1.3 73.6 - - - +
244A VAL* 1.3 63.4 - - - +
246A GLU* 4.1 0.7 - - - +
247A SER* 3.0 31.2 + - - -
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Residues in contact with VAL 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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53A GLN* 3.9 37.3 - - + +
54A VAL* 4.0 6.7 - - + -
240A TRP* 2.9 57.0 + - + +
241A ASN* 4.0 5.8 - - - +
243A ALA* 1.3 75.0 - - - +
245A LYS* 1.3 61.3 + - + +
247A SER* 3.4 1.2 + - - -
248A SER* 2.9 34.6 + - - +
60B THR* 5.9 0.2 - - - +
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Residues in contact with LYS 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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184A SER* 5.6 3.0 + - - -
241A ASN* 3.2 51.3 + - - +
242A VAL* 3.7 16.5 - - - +
244A VAL* 1.3 76.3 - - + +
246A GLU* 1.3 65.4 + - - +
248A SER* 3.1 18.6 + - - -
249A ASN* 3.1 23.7 + - - +
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Residues in contact with GLU 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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55A SER* 4.4 4.9 + - - -
57A LYS* 3.3 31.7 + - - +
58A TRP* 3.6 17.6 + - - +
179A SER* 4.5 7.2 + - - +
180A PRO* 6.3 0.2 - - + -
181A ALA* 3.4 33.9 - - + +
242A VAL 3.0 13.2 + - - +
243A ALA 4.1 0.4 - - - +
245A LYS* 1.3 75.7 - - - +
247A SER* 1.3 65.9 + - - +
249A ASN* 3.3 6.1 + - - +
250A ALA* 2.8 46.0 + - + +
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Residues in contact with SER 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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53A GLN 4.2 4.5 - - - -
54A VAL* 3.5 7.9 - - - -
55A SER* 2.8 44.2 + - - -
58A TRP* 3.7 6.4 - - - -
243A ALA 3.0 18.9 + - - -
244A VAL 3.9 2.5 - - - -
246A GLU* 1.3 83.9 + - - +
248A SER* 1.3 62.1 + - - +
250A ALA* 3.6 2.8 + - - +
251A LYS* 3.3 36.6 + - - +
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Residues in contact with SER 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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53A GLN 5.6 0.2 + - - -
244A VAL* 2.9 20.7 + - - +
245A LYS* 3.1 13.9 + - - -
247A SER* 1.3 76.5 - - - +
249A ASN* 1.3 70.8 + - - +
251A LYS* 3.5 10.5 + - - +
252A LEU* 3.3 30.9 - - - +
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Residues in contact with ASN 249 (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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245A LYS* 3.1 25.3 + - - +
246A GLU* 3.6 4.8 - - - +
248A SER* 1.3 87.2 + - - +
250A ALA* 1.3 61.5 + - - +
252A LEU* 3.2 26.6 + - - +
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Residues in contact with ALA 250 (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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246A GLU* 2.8 34.8 + - - +
247A SER* 4.1 3.8 - - - +
248A SER 3.4 0.2 - - - -
249A ASN* 1.3 73.0 - - - +
251A LYS* 1.3 61.1 + - - +
252A LEU 3.3 3.9 + - - +
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Residues in contact with LYS 251 (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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52A ASP 5.0 8.9 + - - -
53A GLN* 4.9 13.1 + - - +
54A VAL 5.4 2.4 - - - +
55A SER* 5.7 8.3 - - - +
247A SER* 3.3 29.7 + - - +
248A SER* 3.7 11.5 - - - +
249A ASN 3.2 1.0 - - - -
250A ALA* 1.3 75.4 - - - +
252A LEU* 1.3 68.1 + - + +
56B ALA* 5.3 11.1 - - - +
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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