Contacts of the strand formed by residues 208 - 213 (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 VAL 208 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F A2G 3.5 35.7 - - - +
2F GAL 3.7 19.5 - - - +
28H ALA* 3.7 15.9 - - + +
121P MET* 4.9 1.1 - - - -
122P ASP 4.6 2.0 - - - +
124P PRO* 3.4 24.0 - - + -
200P VAL* 3.4 3.9 - - - -
201P CYS 2.8 36.5 + - - +
202P ASN* 4.5 3.1 - - + +
203P GLY* 1.3 77.4 - - - +
209P LEU* 1.3 80.6 + - - +
210P GLN* 4.0 7.2 - - - +
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Residues in contact with LEU 209 (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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29P TRP* 6.4 0.2 - - + -
45P VAL* 4.6 14.1 - - + -
47P VAL* 5.5 1.1 - - + -
53P LEU* 4.7 14.8 - - + -
121P MET* 3.5 35.9 - - + -
122P ASP 4.4 5.3 + - - +
123P LEU* 5.0 12.8 - - + -
124P PRO* 2.9 23.7 - - + +
198P PRO* 3.9 25.4 - - + -
199P LEU 3.8 10.3 - - - +
200P VAL* 3.7 9.6 - - + -
203P GLY 3.6 1.4 + - - -
208P VAL* 1.3 83.5 - - - +
210P GLN* 1.3 68.5 + - - +
211P GLY 3.9 13.0 - - - +
212P ILE* 5.1 2.9 - - + -
231P VAL* 4.6 16.6 - - + -
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Residues in contact with GLN 210 (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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1F A2G 4.5 6.1 + - - -
124P PRO* 3.7 15.7 - - - +
128P GLN 3.1 23.0 - - - +
129P GLU* 3.7 1.2 - - - -
130P PRO* 3.0 45.2 - - + +
181P LEU* 3.3 15.1 - - + +
199P LEU* 3.1 12.4 + - + +
201P CYS* 3.7 29.7 + - + +
208P VAL* 4.0 16.2 - - - +
209P LEU* 1.3 75.7 - - - +
211P GLY* 1.3 60.1 + - - +
230P LYS* 4.1 0.7 - - + +
231P VAL* 3.3 24.5 + - - +
232P VAL* 4.6 4.7 + - + +
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Residues in contact with GLY 211 (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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181P LEU* 4.6 0.4 - - - -
198P PRO* 3.5 4.0 - - - +
199P LEU* 2.8 46.2 + - - +
209P LEU* 3.9 4.3 - - - +
210P GLN* 1.3 79.2 - - - +
212P ILE* 1.3 64.5 + - - -
228P TYR* 4.5 3.1 - - - -
229P THR 3.4 13.5 - - - -
231P VAL* 3.6 8.1 - - - +
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Residues in contact with ILE 212 (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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45P VAL* 5.4 5.2 - - + -
53P LEU* 3.5 43.3 - - + +
54P THR* 4.0 9.0 - - - +
55P ALA* 3.9 18.4 - - + +
102P ASP 4.5 7.4 - - - +
103P LEU* 4.1 15.3 - - + -
196P GLY* 3.9 25.1 - - - +
197P GLY 3.9 2.2 - - - +
198P PRO* 5.2 2.9 - - + -
209P LEU* 5.1 6.1 - - + -
211P GLY* 1.3 76.8 - - - +
213P THR* 1.3 74.4 + - - +
214P SER 3.4 0.2 + - - -
228P TYR* 3.3 3.8 - - - -
229P THR* 2.7 38.9 + - - -
231P VAL* 4.1 8.7 - - + +
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Residues in contact with THR 213 (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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55P ALA* 3.8 6.9 - - - +
57P HIS* 3.9 1.7 - - - -
194P ASP 4.8 3.4 + - - +
195P SER* 4.4 11.0 - - - +
196P GLY* 3.5 27.0 + - - +
197P GLY* 2.9 21.6 + - - -
212P ILE* 1.3 79.9 - - - +
214P SER* 1.3 74.3 + - - +
217P SER* 3.5 18.6 - - - +
218P GLU* 5.3 3.1 - - - -
219P PRO* 5.4 7.1 - - + +
226P SER* 6.1 0.4 - - - -
228P TYR* 3.2 28.5 - - + -
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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