Contacts of the strand formed by residues 180 - 184 (chain P) in PDB entry 3QUM
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 MET 180 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P SER 3.9 20.9 - - - +
100P SER* 4.6 5.2 - - - +
165P ASN* 3.1 18.3 + - - +
174P GLN* 4.2 4.7 - - - +
175P LYS 3.0 14.1 - - - +
176P VAL* 2.9 46.9 - - + -
177P THR* 3.1 26.2 + - + +
178P LYS* 3.2 16.8 + - - +
179P PHE* 1.3 86.8 - - + +
181P LEU* 1.3 62.9 + - - +
214P SER* 5.0 10.5 - - - -
227P LEU* 4.1 19.3 - - + -
228P TYR 3.2 10.5 - - - +
229P THR* 5.8 1.3 - - - -
230P LYS* 4.1 2.6 - - - +
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Residues in contact with LEU 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P GLU* 4.7 2.2 - - - +
130P PRO* 3.7 30.5 - - + +
162P VAL* 4.8 16.4 - - + -
165P ASN* 4.2 0.9 - - - -
178P LYS* 4.5 6.5 - - - +
180P MET* 1.3 74.9 - - - +
182P CYS* 1.3 61.7 + - - +
183P ALA* 4.3 0.9 - - + -
199P LEU* 3.9 22.4 - - + -
210P GLN* 3.3 33.9 - - + +
211P GLY* 4.6 2.2 - - - -
227P LEU* 3.5 2.9 - - - +
228P TYR* 2.7 38.4 + - + +
230P LYS* 3.7 30.4 - - + +
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Residues in contact with CYS 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P VAL* 4.0 4.0 - - - +
163P ILE* 3.1 38.7 + - - +
164P SER 4.0 10.5 - - - +
165P ASN* 3.8 11.7 + - - +
168P CYS* 2.1 53.6 - - - -
181P LEU* 1.3 75.6 - - - +
183P ALA* 1.3 61.8 + - - +
225P PRO* 3.7 18.6 - - - -
226P SER 3.5 7.0 - - - +
227P LEU* 4.4 1.8 - - + -
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Residues in contact with ALA 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P LEU* 4.0 13.9 - - + +
161P HIS* 3.3 23.6 - - - +
162P VAL* 3.9 10.8 - - + -
163P ILE* 3.8 2.5 - - - -
181P LEU* 4.3 1.5 + - + -
182P CYS* 1.3 74.7 - - - +
184P GLY* 1.3 58.2 + - - +
199P LEU* 4.3 14.4 - - + -
225P PRO* 4.4 0.7 - - - -
226P SER* 3.1 27.3 + - - +
228P TYR* 4.2 17.9 - - + -
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Residues in contact with GLY 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P LEU* 3.5 4.6 - - - +
161P HIS* 3.2 21.9 + - - +
163P ILE* 3.2 23.7 - - - +
183P ALA* 1.3 73.4 - - - +
185P ARG* 1.3 75.6 + - - +
186P TRP* 5.8 0.2 - - - -
225P PRO* 3.7 17.7 - - - -
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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