Contacts of the strand formed by residues 215 - 221 (chain D) in PDB entry 5LEZ
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 215 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D VAL 3.3 14.1 - - - +
51D GLU* 4.4 0.4 - - - -
52D LYS* 3.7 12.9 - - - -
199D LEU* 3.3 33.7 - - + -
202D LEU* 4.1 8.5 - - + -
206D MET* 3.7 26.0 - - - -
210D LEU* 3.7 20.4 - - + -
211D ASN 3.4 16.6 - - - +
212D ALA 4.3 0.5 - - - +
213D THR* 4.2 3.5 - - - +
214D ASN* 1.3 85.3 - - - +
216D GLU* 1.3 67.5 + - - +
234D LEU* 3.9 33.0 - - + +
238D ILE* 4.4 5.2 - - + -
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Residues in contact with GLU 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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49D ALA* 3.2 5.4 - - - +
50D VAL* 2.9 43.3 + - + +
52D LYS* 3.2 34.6 + - + +
64D ILE* 2.8 22.4 - - - +
65D GLU* 4.1 2.3 - - - +
66D LYS* 3.2 18.2 + - - +
67D ILE* 3.1 35.4 + - + +
215D ILE* 1.3 77.9 - - - +
217D LEU* 1.3 60.9 + - - +
228D MET* 4.2 15.1 - - + +
234D LEU* 4.9 3.1 - - - -
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Residues in contact with LEU 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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47D CYS* 4.6 8.1 - - + -
48D LEU 3.3 15.7 - - - +
49D ALA* 3.7 17.7 - - + -
67D ILE* 4.0 2.5 - - - -
195D ILE* 3.8 28.7 - - + -
198D SER* 4.4 6.1 - - - +
199D LEU* 4.3 13.2 - - + -
216D GLU* 1.3 75.9 - - - +
218D ALA* 1.3 61.2 + - - +
219D THR* 4.7 1.8 - - + -
228D MET* 3.7 5.7 - - - +
229D PHE* 2.8 79.9 + - + +
234D LEU* 3.9 20.7 - - + +
237D VAL* 5.7 0.2 - - + -
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Residues in contact with ALA 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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47D CYS* 3.3 4.2 - - - +
48D LEU* 2.9 35.9 + - + +
67D ILE* 3.7 18.8 - - + +
217D LEU* 1.3 75.7 - - - +
219D THR* 1.3 66.2 + - - +
226D PHE* 3.7 30.5 - - + -
227D HIS 3.2 13.5 - - - +
228D MET* 4.2 4.0 - - - -
229D PHE* 4.6 0.9 - - - +
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Residues in contact with THR 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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46D VAL* 3.3 9.0 - - - +
47D CYS* 3.9 16.8 - - + -
191D LEU* 4.3 8.3 - - + -
195D ILE* 4.0 22.0 - - + -
217D LEU* 4.7 0.9 - - + -
218D ALA* 1.3 80.3 - - - +
220D VAL* 1.3 69.7 + - - +
221D GLN* 4.1 21.3 + - - +
224D GLN* 4.8 0.3 + - - -
225D ASN 4.1 0.6 - - - +
226D PHE* 3.4 2.0 - - - -
227D HIS* 2.9 43.7 + - - +
229D PHE* 4.0 16.0 - - + -
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Residues in contact with VAL 220 (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 GLY* 3.1 3.3 - - - -
46D VAL* 3.0 33.6 + - + +
48D LEU* 6.2 1.3 - - + -
73D HIS* 3.6 29.6 - - + +
75D GLY* 4.2 3.8 - - - +
144D GLY 3.8 20.9 - - - +
145D GLY* 4.1 7.9 - - - +
146D VAL* 3.7 18.9 - - + +
219D THR* 1.3 80.2 - - - +
221D GLN* 1.3 67.1 + - - +
224D GLN 4.0 11.2 - - - +
225D ASN 4.7 0.7 - - - -
226D PHE* 3.9 27.8 - - + +
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Residues in contact with GLN 221 (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 GLU* 3.6 6.6 - - - +
146D VAL* 3.7 9.6 - - - +
191D LEU* 3.6 30.2 - - + +
219D THR* 4.1 11.7 + - - +
220D VAL* 1.3 82.7 - - - +
222D PRO* 1.3 76.0 - - + +
223D GLY* 4.2 5.6 - - - +
224D GLN* 2.8 59.6 + - + +
225D ASN 5.1 0.2 + - - -
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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