Contacts of the helix formed by residues 212 - 221 (chain B) 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 ARG 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.3 19.5 - - - +
337A GLY 3.0 23.1 + - - -
338A THR* 2.8 32.3 + - + +
339A GLY 3.8 8.5 + - - -
340A ASN* 5.6 4.8 - - - +
366A ARG* 4.4 16.0 - - - +
211B GLU* 1.3 81.4 + - - +
213B PRO* 1.3 70.3 - - + +
214B GLU* 3.3 19.3 - - - +
215B GLU* 3.1 42.1 + - + +
216B VAL* 3.1 21.9 + - - +
232B PHE* 3.8 11.2 - - + -
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Residues in contact with PRO 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 3.7 21.4 - - + +
173A ARG* 6.1 0.2 - - - +
302A GLY 5.3 2.0 - - - +
305A ARG* 3.4 27.4 - - - +
211B GLU 3.7 0.9 - - - +
212B ARG* 1.3 85.8 - - + +
214B GLU* 1.3 70.3 + - - +
216B VAL* 3.1 13.3 + - + +
217B THR* 3.1 16.5 + - - +
231B THR* 3.8 28.5 - - + -
232B PHE* 3.6 18.6 - - + -
233B ASP* 4.4 6.3 - - - +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 3.4 37.6 - - + +
139A LEU* 4.1 16.0 - - - +
140A HIS* 4.9 15.9 + - + +
173A ARG* 2.6 43.4 + - - +
302A GLY 5.5 0.7 - - - +
305A ARG* 4.1 8.6 + - - +
212B ARG* 3.3 17.8 - - + +
213B PRO* 1.3 84.5 - - - +
215B GLU* 1.3 67.4 + - + +
217B THR* 3.3 8.6 - - - +
218B GLU* 3.2 25.6 + - - +
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A HIS* 5.3 8.6 - - + -
185B THR* 5.0 16.4 + - + -
208B LEU* 5.0 4.3 - - + -
211B GLU* 3.6 26.2 - - + +
212B ARG* 3.1 51.6 + - + +
214B GLU* 1.3 79.0 - - + +
216B VAL* 1.3 65.0 + - - +
218B GLU* 3.7 12.2 - - - +
219B MET* 3.1 32.4 + - + +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 4.7 8.3 - - + +
211B GLU* 4.8 12.1 - - + -
212B ARG 3.1 15.6 + - - +
213B PRO* 3.1 8.5 + - + +
215B GLU* 1.3 78.4 - - - +
217B THR* 1.3 58.8 + - - +
218B GLU 3.3 0.2 + - - -
219B MET* 3.4 2.6 + - - +
220B GLN* 3.1 34.1 + - - +
227B VAL* 4.5 5.3 - - + +
229B ALA* 3.7 33.0 - - + -
230B SER 5.1 0.2 - - - +
231B THR* 4.0 23.6 - - + +
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Residues in contact with THR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A THR* 4.1 12.3 - - - +
138A PRO* 3.3 38.1 - - + +
139A LEU* 5.1 4.7 - - + +
213B PRO 3.1 11.3 + - - +
214B GLU* 3.3 13.0 - - - +
216B VAL* 1.3 79.3 - - - +
218B GLU* 1.3 61.5 + - - +
220B GLN* 3.9 11.8 + - - +
221B ARG* 3.4 47.5 + - - +
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 6.0 5.6 - - + -
140A HIS* 3.0 31.7 + - - -
185B THR* 4.6 6.7 - - - +
186B MET* 5.8 1.4 - - - +
189B GLN* 3.0 29.4 + - - +
214B GLU 3.2 17.6 + - - +
215B GLU* 3.7 10.5 - - - +
216B VAL 3.2 0.6 - - - -
217B THR* 1.3 76.2 - - + +
219B MET* 1.3 66.6 + - - +
221B ARG* 3.4 4.9 + - - +
222B LEU* 3.2 31.4 + - + +
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Residues in contact with MET 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B THR* 4.9 7.9 - - - +
188B LEU* 3.8 27.8 - - + -
189B GLN* 3.5 44.0 - - + -
206B VAL* 5.0 8.1 - - + -
208B LEU* 3.8 24.2 - - + -
215B GLU* 3.1 19.9 + - + +
216B VAL 4.0 2.9 - - - +
218B GLU* 1.3 78.1 - - + +
220B GLN* 1.3 62.3 + - - +
222B LEU* 4.3 2.7 - - - -
223B VAL* 3.2 53.2 + - + +
227B VAL* 4.2 7.9 - - + -
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASP* 5.5 7.7 + - - +
216B VAL* 3.1 23.4 + - - +
217B THR* 4.0 11.9 + - - +
218B GLU 3.2 0.4 - - - -
219B MET* 1.3 80.1 - - - +
221B ARG* 1.3 63.3 + - + +
222B LEU 3.4 0.9 + - - -
223B VAL 4.1 9.2 - - - +
225B GLY 5.5 1.2 - - - +
227B VAL* 3.7 34.5 + - + +
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A THR* 3.4 28.4 + - - +
139A LEU* 6.0 2.2 - - - +
308A GLU* 3.4 26.1 + - - -
309A GLU* 5.2 2.6 + - - -
217B THR* 3.4 28.4 + - - +
218B GLU* 3.4 5.5 + - - +
219B MET 3.2 0.4 - - - -
220B GLN* 1.3 82.9 - - + +
222B LEU* 1.3 57.9 + - - +
223B VAL 4.9 0.9 - - - -
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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