Contacts of the strand formed by residues 190 - 195 (chain H) in PDB entry 2QC8
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 190 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G THR* 2.6 30.5 + - - +
179H HIS* 4.1 20.6 - - + +
180H TYR* 3.8 42.4 - - + -
183H CYS* 3.9 14.6 - - + -
184H LEU* 3.8 30.4 - - + +
188H VAL 2.8 15.8 + - - +
189H LYS* 1.3 70.8 - - - +
191H ALA* 1.3 54.9 + - - +
192H GLY 4.0 8.1 - - - +
193H THR* 4.3 2.9 - - + -
204H PHE* 4.1 16.4 - - + -
205H GLN 3.5 12.6 - - - +
206H ILE* 3.7 8.3 - - + +
207H GLY 5.0 0.2 - - - -
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Residues in contact with ALA 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ARG* 3.4 7.1 - - - +
46G THR* 2.9 29.5 + - - +
189H LYS 3.5 1.2 + - - -
190H ILE* 1.3 71.9 - - - +
192H GLY* 1.3 57.1 + - - +
205H GLN* 2.9 23.1 + - + +
207H GLY 3.6 14.8 - - - +
208H PRO* 5.4 0.2 - - + -
501H ADP 3.5 27.8 - - - +
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Residues in contact with GLY 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G THR 3.1 14.4 - - - -
45G ARG* 3.9 0.2 - - - -
60G TRP* 5.8 0.4 - - - -
180H TYR* 3.5 13.0 + - - -
190H ILE* 3.6 4.1 - - - +
191H ALA* 1.3 80.3 - - - +
193H THR* 1.3 69.0 + - - +
204H PHE* 3.5 1.6 - - - +
205H GLN* 3.1 35.6 + - - +
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Residues in contact with THR 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G LYS* 3.4 2.0 - - - +
44G THR* 2.9 31.5 + - - +
90G ARG* 4.6 0.7 + - - -
708G CL 3.3 14.7 - - - +
176H VAL* 4.1 24.0 - - + +
179H HIS* 5.8 1.1 - - - +
180H TYR* 3.3 36.3 - - + -
190H ILE* 4.3 3.6 - - + -
192H GLY* 1.3 79.9 - - - +
194H ASN* 1.3 66.8 + - - +
203H GLU 3.1 16.2 - - - +
204H PHE* 3.8 12.3 - - + -
205H GLN* 3.5 3.9 + - - -
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Residues in contact with ASN 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G LYS* 3.5 28.7 + - + +
708G CL 4.2 4.9 - - - -
162H TYR* 4.2 8.0 - - - -
163H CYS* 4.0 6.3 - - - -
193H THR* 1.3 76.8 - - - +
195H ALA* 1.3 82.1 + - - +
196H GLU* 3.4 11.7 + - - -
202H TRP* 3.7 6.1 - - - -
203H GLU* 2.9 70.5 + - - +
205H GLN* 3.2 10.9 + - - -
403H MN 4.1 2.6 + - - -
601H P3S 4.7 1.8 + - - -
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Residues in contact with ALA 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G CYS 5.0 0.8 + - - -
161H TYR 3.6 11.0 - - - +
162H TYR* 3.8 3.3 - - - -
163H CYS* 2.9 37.6 + - - +
164H GLY 3.9 8.1 - - - +
169H ARG 5.8 0.4 - - - +
170H ALA* 5.6 2.7 - - + -
173H ARG* 5.7 0.9 - - - +
194H ASN* 1.3 83.9 + - - +
196H GLU* 1.3 59.5 + - - +
201H GLN 4.7 0.9 - - - +
202H TRP* 3.5 40.4 - - + -
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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