Contacts of the helix formed by residues 212 - 229 (chain K) in PDB entry 6XAV
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 ASP 212 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91K ARG* 4.9 2.6 - - - +
205K MET* 5.1 0.2 - - - -
211K ILE* 1.3 79.5 - - - +
213K PRO* 1.3 77.9 - - - +
214K GLU* 3.1 33.1 + - - +
215K GLU* 3.2 34.6 + - - +
216K ALA* 3.1 23.7 + - - +
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Residues in contact with PRO 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ILE* 4.1 15.3 - - + -
18K GLN* 4.1 15.3 - - - +
24K ALA* 3.7 23.6 - - + -
26K VAL* 4.1 17.9 - - + -
205K MET* 3.6 22.6 - - - +
207K THR* 6.4 0.7 - - + -
211K ILE 4.3 4.0 - - - +
212K ASP* 1.3 95.8 - - - +
214K GLU* 1.3 62.9 + - - +
216K ALA* 3.2 3.6 + - - +
217K ILE* 3.2 29.3 + - - +
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Residues in contact with GLU 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K LEU* 4.0 14.9 - - + +
16K ILE* 3.8 21.8 - - + +
212K ASP* 3.1 12.5 + - - +
213K PRO* 1.3 78.8 - - - +
215K GLU* 1.3 61.9 + - + +
216K ALA 3.1 0.2 + - - -
217K ILE* 3.3 3.4 + - - +
218K ARG* 3.0 68.4 + - - +
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Residues in contact with GLU 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K MET* 4.8 0.3 - - - +
91K ARG* 5.2 5.5 + - - -
211K ILE* 5.0 9.1 - - + +
212K ASP* 3.2 39.3 + - + +
214K GLU* 1.3 80.7 - - + +
216K ALA* 1.3 56.1 + - - +
218K ARG* 5.1 3.1 - - - +
219K ARG* 3.2 31.5 + - - +
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Residues in contact with ALA 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K LEU* 3.2 28.5 - - + +
51K MET* 3.9 9.5 - - + +
180K VAL* 5.4 3.4 - - + -
205K MET* 4.4 12.6 - - + -
211K ILE* 3.8 19.7 - - + -
212K ASP 3.1 15.1 + - - +
213K PRO 3.7 4.3 - - - +
214K GLU 3.1 0.4 - - - -
215K GLU* 1.3 80.5 - - - +
217K ILE* 1.3 59.4 + - - +
219K ARG* 3.8 1.7 - - - +
220K ALA 3.0 21.1 + - - -
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Residues in contact with ILE 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H PHE* 3.9 28.0 - - + +
13K LEU* 5.4 4.0 - - + -
26K VAL* 3.7 43.5 - - + -
28K LEU* 4.3 11.2 - - + -
43K LEU* 4.6 20.2 - - + +
47K LEU* 4.9 8.5 - - + -
203K ILE* 4.4 9.9 - - + -
205K MET* 3.8 14.6 - - + -
213K PRO 3.2 13.6 + - - +
214K GLU* 4.2 4.7 - - - +
216K ALA* 1.3 72.8 - - - +
218K ARG* 1.3 62.2 + - + +
219K ARG 3.1 4.7 - - - -
220K ALA* 4.2 2.6 - - - +
221K ALA* 3.1 26.0 + - + +
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Residues in contact with ARG 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H ALA 3.1 26.9 + - - -
231H PHE* 3.3 40.2 + - + +
232H VAL 5.0 3.4 + - - -
13K LEU* 4.1 22.9 - - + +
214K GLU* 3.0 52.7 + - + +
215K GLU* 5.1 2.9 - - - +
217K ILE* 1.3 74.6 - - - +
219K ARG* 1.3 51.6 + - - +
222K THR* 2.4 32.8 + - - -
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Residues in contact with ARG 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H VAL* 5.3 2.4 - - - +
6H THR* 4.2 22.7 + - + +
51K MET* 3.8 22.0 - - + -
52K PRO* 3.3 33.6 - - - +
148K ARG* 6.0 0.8 - - - +
211K ILE* 5.8 0.9 - - - -
215K GLU* 3.2 22.5 + - - +
216K ALA* 3.5 5.5 + - - +
217K ILE 3.1 0.6 - - - -
218K ARG* 1.3 78.0 - - - +
220K ALA* 1.3 63.9 + - - +
221K ALA 3.4 0.4 - - - -
222K THR* 3.4 6.3 + - - -
223K ILE* 3.1 36.0 + - + +
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Residues in contact with ALA 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K LEU* 4.4 11.2 - - + +
46K ILE* 3.6 40.3 - - + +
47K LEU* 3.7 20.4 - - + -
51K MET* 4.7 3.3 - - - -
216K ALA 3.0 17.6 + - - +
217K ILE* 4.2 3.1 - - - +
219K ARG* 1.3 72.8 - - - +
221K ALA* 1.3 61.1 + - - +
223K ILE* 3.1 3.8 + - - +
224K LEU 2.9 24.3 + - - -
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Residues in contact with ALA 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H LEU* 4.0 16.4 - - + +
231H PHE* 3.7 26.0 - - + -
232H VAL* 3.6 8.0 - - + +
43K LEU* 4.1 17.3 - - + +
217K ILE* 3.1 18.7 + - + +
218K ARG 4.7 0.9 - - - +
220K ALA* 1.3 76.8 - - - +
222K THR* 1.3 57.0 + - - +
224K LEU* 3.3 5.3 + - - +
225K ALA* 2.9 30.8 + - - +
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Residues in contact with THR 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H THR* 6.5 1.3 - - + -
232H VAL* 3.7 33.1 + - + +
218K ARG 2.4 24.1 + - - -
219K ARG* 3.4 12.1 + - - -
220K ALA 3.2 0.4 - - - -
221K ALA* 1.3 78.2 - - - +
223K ILE* 1.3 58.1 + - + +
225K ALA* 3.4 2.4 + - - +
226K GLU* 2.8 35.2 + - + +
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Residues in contact with ILE 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H THR* 4.9 8.3 - - + -
8H PHE* 3.6 45.1 - - + -
35H PHE* 4.1 27.6 - - + -
46K ILE* 4.2 13.7 - - + -
50K SER* 4.2 14.8 - - - +
51K MET* 5.2 2.0 - - - -
52K PRO* 5.9 2.7 - - + -
219K ARG* 3.1 27.1 + - + +
220K ALA* 3.1 6.6 + - - +
222K THR* 1.3 77.3 - - + +
224K LEU* 1.3 62.0 + - - +
226K GLU* 3.2 12.9 + - - +
227K GLN* 3.1 24.6 + - + +
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Residues in contact with LEU 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H PHE* 6.5 0.2 - - + -
38H THR* 4.6 11.2 - - + -
39H LEU* 3.7 26.0 - - + -
42H ALA* 5.8 2.0 - - + -
224H LEU* 5.3 6.7 - - + -
228H LEU* 3.6 23.3 - - + -
39K LEU* 5.2 5.2 - - + -
42K ALA* 4.0 24.2 - - + -
43K LEU* 4.6 11.2 - - + -
46K ILE* 3.6 20.6 - - + +
220K ALA 2.9 15.2 + - - +
221K ALA* 3.6 5.6 - - - +
223K ILE* 1.3 77.4 - - - +
225K ALA* 1.3 61.8 + - - +
227K GLN* 3.1 6.5 + - + +
228K LEU* 3.1 36.1 + - + +
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Residues in contact with ALA 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225H ALA* 5.6 8.7 - - + +
228H LEU* 4.4 8.9 - - + +
232H VAL* 4.0 20.0 - - + -
221K ALA 2.9 16.7 + - - +
222K THR 3.9 3.6 - - - +
224K LEU* 1.3 76.1 - - - +
226K GLU* 1.3 62.6 + - - +
227K GLN 3.3 0.5 + - - -
228K LEU* 3.4 19.3 + - + +
229K GLU* 3.5 13.3 + - - +
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Residues in contact with GLU 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H THR* 4.1 24.8 - - - +
8H PHE* 4.5 11.7 + - - -
10H LYS* 3.3 36.4 + - - +
222K THR* 2.8 21.8 + - + +
223K ILE* 3.2 17.1 + - - +
225K ALA* 1.3 76.7 - - - +
227K GLN* 1.3 60.1 + - + +
229K GLU* 3.1 21.4 - - + +
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Residues in contact with GLN 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H PHE* 3.5 23.4 - - - +
9H LEU 3.5 24.5 + - - +
10H LYS* 4.2 13.6 - - - +
11H PRO* 4.2 12.0 - - - +
31H LEU* 5.6 3.6 - - - +
32H GLU* 5.2 0.8 - - - +
35H PHE* 4.2 31.3 - - + -
39H LEU* 3.8 31.1 - - + +
223K ILE* 3.1 14.7 + - + +
224K LEU* 3.1 10.1 + - + +
226K GLU* 1.3 81.2 + - - +
228K LEU* 1.3 59.7 + - - +
229K GLU* 3.2 6.5 + - - -
230K ALA* 3.6 17.4 + - - +
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Residues in contact with LEU 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU* 3.8 26.2 - - + +
42H ALA* 5.7 0.7 - - + -
43H LEU* 6.0 6.1 - - + -
221H ALA* 4.6 17.7 - - + +
224H LEU* 3.7 44.9 - - + +
225H ALA* 4.3 18.6 - - + +
228H LEU* 4.7 2.9 - - + -
224K LEU* 3.1 32.4 + - + +
225K ALA* 3.4 9.8 + - - +
227K GLN* 1.3 73.5 - - - +
229K GLU* 1.3 59.7 + - - +
230K ALA* 3.1 7.8 + - - -
231K PHE* 3.4 25.3 - - - +
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Residues in contact with GLU 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H LYS* 3.6 29.3 - - - +
225K ALA 3.5 8.4 + - - +
226K GLU* 3.1 21.9 - - + +
227K GLN 4.6 0.2 - - - -
228K LEU* 1.3 74.5 - - - +
230K ALA* 1.3 65.9 + - - +
231K PHE* 2.9 32.1 + - + -
232K VAL* 4.3 8.1 - - - +
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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