Contacts of the strand formed by residues 211 - 219 (chain D) in PDB entry 5GJQ
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 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D ALA 3.5 6.7 - - - +
48D GLU* 5.6 0.9 - - - -
49D ARG* 3.7 7.4 + - - -
197D LEU* 4.1 27.4 - - + -
206D LEU* 4.1 32.5 - - + -
207D SER 4.0 9.6 - - - +
208D ALA* 2.9 17.8 + - - +
210D LYS* 1.3 86.5 - - + +
212D GLU* 1.3 63.1 + - - +
213D ILE* 4.6 10.5 - - + -
233D VAL* 3.7 30.8 - - + +
237D ILE* 4.9 4.7 - - + -
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Residues in contact with GLU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU 4.0 0.7 - - - +
46D ALA* 3.2 2.8 - - - -
47D ALA* 2.9 39.8 + - + +
49D ARG* 3.8 21.2 + - + +
58D GLU* 5.3 1.9 - - - +
61D PHE 4.8 0.2 - - - +
62D SER* 2.7 32.6 + - - +
63D GLU* 3.0 24.0 + - - +
64D LYS* 3.0 21.3 + - - +
65D ILE* 3.9 12.3 - - + +
211D VAL* 1.3 77.0 - - - +
213D ILE* 1.3 63.8 + - - +
227D VAL* 4.5 15.6 - - + +
233D VAL* 6.2 0.7 - - - -
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.1 7.9 - - + -
45D LEU 3.4 9.4 - - - +
46D ALA* 4.2 15.3 - - + -
190D LEU* 3.8 20.4 - - + +
193D ALA* 4.6 12.6 - - + -
194D ILE* 5.2 7.4 - - + +
197D LEU* 4.9 6.1 - - + -
211D VAL* 4.6 13.7 - - + -
212D GLU* 1.3 82.7 - - - +
214D ALA* 1.3 68.1 + - - +
215D THR* 5.0 0.2 - - + -
227D VAL* 3.3 8.6 - - - +
228D LEU* 2.9 56.6 + - + -
233D VAL* 4.8 14.6 - - + +
236D LEU* 5.7 7.6 - - + -
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Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.2 6.6 - - - +
45D LEU* 2.8 38.8 + - + +
65D ILE* 3.9 33.0 - - + -
137D ILE* 5.2 4.6 - - + +
213D ILE* 1.3 75.8 - - - +
215D THR* 1.3 64.4 + - - +
225D ILE* 5.4 4.7 - - + -
226D ARG 3.2 11.4 - - - +
227D VAL* 4.0 8.7 - - + -
228D LEU* 5.1 0.7 - - - -
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Residues in contact with THR 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL 3.5 4.5 - - - -
44D LEU* 3.8 14.8 - - + -
137D ILE* 5.2 1.8 - - - -
186D LEU* 3.8 29.0 - - + +
190D LEU* 4.5 19.1 - - + -
214D ALA* 1.3 79.7 - - - +
216D LEU* 1.3 62.0 + - - +
217D THR* 4.2 6.2 + - - +
224D VAL 3.8 0.9 - - - +
225D ILE* 3.3 7.1 - - - +
226D ARG* 2.8 54.7 + - - +
228D LEU* 4.4 11.6 - - + +
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLY* 3.2 5.2 - - - -
43D VAL* 2.8 43.9 + - + +
71D ASP 3.8 13.2 - - - +
72D MET* 4.3 0.2 - - - -
137D ILE* 3.8 39.0 - - + +
138D GLY* 3.9 4.9 - - - -
139D TRP* 4.2 12.6 - - + -
145D PHE* 3.5 24.0 - - + -
215D THR* 1.3 74.8 - - - +
217D THR* 1.3 64.9 + - - +
223D THR* 3.9 16.6 - - + -
224D VAL 3.4 3.1 - - - -
225D ILE* 3.7 30.1 - - + +
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Residues in contact with THR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASP 3.4 19.5 - - - +
42D GLY* 4.0 2.0 - - - -
145D PHE* 4.0 9.2 - - - -
186D LEU* 3.7 28.9 - - + -
215D THR* 4.8 7.1 + - - +
216D LEU* 1.3 83.4 + - - +
218D ARG* 1.3 62.3 + - - +
219D GLU* 3.9 20.0 + - - -
223D THR* 3.7 4.9 - - - +
224D VAL* 2.9 40.4 + - - +
226D ARG* 5.2 2.9 + - - +
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Residues in contact with ARG 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASP 4.8 1.8 + - - -
71D ASP* 4.9 2.6 + - - -
139D TRP* 3.2 65.5 - - + +
145D PHE* 3.9 15.7 - - + -
217D THR* 1.3 76.7 - - - +
219D GLU* 1.3 62.4 + - - +
220D ASN 4.4 0.4 + - - -
221D GLY* 2.7 41.1 + - - -
222D LYS* 3.6 8.7 + - - +
223D THR* 2.8 27.7 + - - +
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Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D THR* 3.9 13.5 + - - +
218D ARG* 1.3 80.9 - - - +
220D ASN* 1.3 74.4 + - + +
221D GLY 3.3 1.1 - - - -
222D LYS* 3.0 26.3 + - - +
224D VAL* 3.6 27.2 - - + +
226D ARG* 3.3 25.3 + - - -
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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