Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 1QQG
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 ILE 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A SER* 4.1 3.9 - - - -
192B ILE* 3.9 30.7 - - + -
206B LEU* 5.2 4.7 - - + -
207B GLN 3.8 11.0 - - - +
208B LEU* 3.3 30.1 + - + +
209B MET 3.4 1.3 - - - +
210B ASN* 1.3 77.5 - - - +
212B ARG* 1.3 60.9 + - - +
213B ARG 3.4 20.0 - - - +
214B CYS* 4.7 2.2 - - + -
223B ILE* 3.5 22.4 - - + -
224B GLU 3.2 16.4 - - - +
225B VAL* 4.0 7.6 - - + +
253B ILE* 4.8 1.6 - - + -
257B MET* 3.3 30.4 - - + +
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Residues in contact with ARG 212 (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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255A GLU* 2.7 44.4 + - - -
258A ARG* 2.9 55.0 + - - +
259A ALA* 3.1 12.7 - - - +
261A SER* 2.8 24.2 - - - +
262A ASP* 2.8 41.8 + - - -
210B ASN 3.5 2.2 + - - -
211B ILE* 1.3 72.9 - - - +
213B ARG* 1.3 61.5 + - + +
224B GLU* 2.9 38.2 + - + +
225B VAL 4.8 0.9 - - - -
226B GLY* 3.7 12.6 - - - -
257B MET* 4.4 4.2 - - - +
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Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 3.6 43.2 - - - +
211B ILE* 3.3 9.0 - - - +
212B ARG* 1.3 82.6 - - - +
214B CYS* 1.3 62.9 + - - +
215B GLY* 5.7 0.4 - - - -
222B PHE* 3.8 32.1 - - + -
224B GLU* 2.7 67.1 + - + +
235B GLU* 5.1 2.8 + - - -
257B MET* 4.3 6.5 - - - -
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Residues in contact with CYS 214 (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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258A ARG* 5.8 0.5 + - - -
211B ILE* 4.7 5.8 - - + -
213B ARG* 1.3 82.6 + - - +
215B GLY* 1.3 58.4 + - - +
221B PHE* 3.9 15.7 - - + -
222B PHE* 3.2 22.1 - - - +
223B ILE* 4.4 6.1 - - + -
250B HIS* 3.2 49.3 - - - -
253B ILE* 4.4 5.4 - - + -
254B LEU* 4.3 14.8 - - - -
257B MET* 4.3 13.0 - - - +
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Residues in contact with GLY 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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213B ARG* 5.7 0.9 - - - -
214B CYS* 1.3 77.3 - - - +
216B HIS* 1.3 62.2 + - - -
221B PHE* 3.0 11.6 - - - -
222B PHE* 2.7 54.7 + - - -
250B HIS* 3.9 10.8 - - - -
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Residues in contact with HIS 216 (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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215B GLY* 1.3 74.4 - - - +
217B SER* 1.3 63.0 + - - +
218B GLU 4.5 5.6 - - - -
220B PHE 3.1 17.9 - - - +
221B PHE* 4.1 1.1 - - - +
222B PHE* 3.8 6.8 - - - -
243B SER* 4.4 6.7 - - - -
246B ALA* 3.7 22.0 - - + +
247B GLN* 3.7 41.3 + - + +
250B HIS* 3.7 29.7 - + + +
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Residues in contact with SER 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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216B HIS* 1.3 74.1 - - - +
218B GLU* 1.3 85.2 + - - +
220B PHE* 3.0 29.7 + - - +
222B PHE* 5.5 1.7 - - - -
237B TRP* 5.0 12.5 - - - -
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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