Contacts of the strand formed by residues 213 - 224 (chain L) in PDB entry 1DZG
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 LEU 213 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146L LEU* 4.2 12.8 - - + -
147L PHE 3.3 24.5 - - - +
148L GLY* 3.6 16.4 - - - +
154L PHE* 4.3 7.4 - - + -
158L TYR* 3.8 19.1 - - + +
170L LEU* 4.8 4.0 - - + -
175L PHE* 4.3 0.2 - - - -
211L THR* 3.8 1.2 - - - +
212L VAL* 1.3 88.1 - - + +
214L VAL* 1.3 67.6 + - - +
215L LEU* 4.0 13.0 - - + -
354L ILE* 3.8 22.7 - - + -
389L VAL* 3.9 1.6 - - - +
390L ILE* 2.8 60.7 + - + +
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Residues in contact with VAL 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L ARG 3.5 0.5 - - - +
147L PHE* 2.9 43.0 + - + +
175L PHE* 3.6 26.2 - - + -
186L ILE* 3.6 17.9 - - + -
202L ILE* 4.0 22.0 - - + -
207L ILE* 4.1 3.8 - - + -
211L THR* 4.3 0.4 - - + -
213L LEU* 1.3 72.9 - - - +
215L LEU* 1.3 63.7 + - - +
216L VAL* 4.0 15.5 - - + -
387L ALA* 4.3 4.7 - - + -
388L VAL 3.3 12.8 - - - +
389L VAL* 3.6 25.1 - - + -
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Residues in contact with LEU 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ALA* 4.9 1.5 - - - +
89L MET* 3.8 16.2 - - + -
90L THR* 3.5 37.7 - - + +
145L ARG 3.9 3.6 - - - -
146L LEU* 3.5 26.9 - - + -
158L TYR* 3.6 14.1 - - - +
213L LEU* 4.0 6.5 - - + -
214L VAL* 1.3 71.7 - - - +
216L VAL* 1.3 59.1 + - - +
354L ILE* 6.3 0.9 - - + -
386L THR 3.8 0.5 - - - +
387L ALA* 3.1 4.9 - - - -
388L VAL* 2.8 62.8 + - + +
390L ILE* 3.9 28.7 - - + -
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Residues in contact with VAL 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L ALA* 5.2 0.2 - - - -
89L MET* 3.4 10.5 - - - +
144L ASN* 3.3 5.7 - - - -
145L ARG 3.0 36.3 + - - +
147L PHE* 3.8 11.2 - - + -
186L ILE* 3.8 27.6 - - + -
189L TRP* 3.4 25.6 - - + -
190L VAL* 3.5 19.3 - - + -
214L VAL* 4.0 6.1 - - + -
215L LEU* 1.3 78.2 - - - +
217L ASN* 1.3 69.6 + - - +
385L SER* 3.9 2.2 - - - +
386L THR 3.3 4.3 - - - +
387L ALA* 3.9 14.8 - - + -
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Residues in contact with ASN 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L SER* 3.0 44.7 + - - +
85L THR* 3.1 20.3 + - - +
86L ALA* 4.1 11.9 - - + +
142L SER* 3.3 9.4 + - - -
143L ALA 3.3 1.5 - - - +
144L ASN* 3.1 20.7 + - - +
216L VAL* 1.3 74.8 - - - +
218L THR* 1.3 82.0 + - - +
219L ILE* 4.4 4.9 - - - +
385L SER* 2.7 29.2 + - - -
386L THR 2.8 19.6 + - - +
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Residues in contact with THR 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L VAL* 4.9 1.6 - - + +
142L SER* 2.7 38.6 + - - -
143L ALA* 2.8 24.4 + - + +
189L TRP* 4.3 8.0 - - - -
190L VAL* 4.0 6.1 - - - +
193L LYS* 3.6 39.6 - - + +
194L THR* 3.9 15.4 - - + +
217L ASN* 1.3 85.6 + - - +
219L ILE* 1.3 63.0 + - - +
220L TYR* 4.9 0.7 - - + +
384L ALA 3.5 4.7 - - - -
385L SER* 3.4 9.7 + - - -
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Residues in contact with ILE 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L SER* 3.6 10.1 - - - +
81L LEU* 4.0 12.1 - - + -
82L SER* 3.6 37.2 + - - +
85L THR* 5.4 0.4 - - - +
131L TYR* 3.6 24.0 - - - +
140L LEU* 3.6 25.4 - - + -
141L VAL 3.3 4.0 - - - +
142L SER* 4.1 6.1 - - - +
194L THR* 4.3 2.3 - - - +
217L ASN* 4.4 4.9 - - - +
218L THR* 1.3 80.4 - - - +
220L TYR* 1.3 64.1 + - - +
383L ALA* 3.4 2.3 - - - +
384L ALA* 2.9 36.1 + - + +
421L ILE* 3.7 5.6 - - + -
422L PHE* 3.7 21.1 - - + -
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Residues in contact with TYR 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L LYS* 3.3 29.2 - - + +
140L LEU* 3.3 6.7 - - - -
141L VAL* 2.9 48.8 + - + -
193L LYS 4.2 11.0 - - - +
194L THR* 3.6 26.0 - - - -
195L GLU* 3.5 30.5 - - + +
197L ARG* 4.3 2.7 - - + -
218L THR* 5.3 0.2 - - + -
219L ILE* 1.3 76.6 - - - +
221L PHE* 1.3 75.0 + - - +
222L LYS* 3.6 18.3 + - + -
381L GLU* 2.7 37.0 + - + -
382L ALA 3.8 2.5 - - - -
383L ALA* 3.7 12.6 - - + -
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Residues in contact with PHE 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L SER* 4.0 9.9 - - - -
139L LYS 3.2 12.1 - - - -
140L LEU* 4.0 10.1 - - + -
220L TYR* 1.3 84.7 - - - +
222L LYS* 1.3 65.1 + - - +
223L GLY* 3.4 29.2 - - - -
274L PHE* 3.8 37.0 - + - -
279L ILE* 3.5 40.6 - - + -
380L SER* 3.9 7.6 - - - -
381L GLU* 3.6 4.2 - - - +
382L ALA 2.8 39.5 + - - +
412L ILE* 4.3 17.0 - - + -
421L ILE* 5.3 1.3 - - + -
422L PHE* 3.6 21.9 - + + -
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Residues in contact with LYS 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L SER 4.9 0.5 - - - +
138L SER* 3.7 2.9 - - - -
139L LYS* 3.1 38.9 + - + +
220L TYR* 3.6 21.7 + - + -
221L PHE* 1.3 81.9 - - - +
223L GLY* 1.3 66.6 + - - +
224L LEU* 5.4 8.1 - - + -
380L SER 3.4 10.8 - - - +
381L GLU* 3.4 27.7 + - + +
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Residues in contact with GLY 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L SER 5.5 0.2 - - - -
138L SER* 4.2 10.1 - - - -
221L PHE* 3.4 22.4 - - - -
222L LYS* 1.3 77.7 - - - +
224L LEU* 1.3 72.4 + - - +
274L PHE* 3.6 9.9 - - - -
379L GLY* 3.6 0.5 - - - -
380L SER 3.0 26.8 + - - +
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Residues in contact with LEU 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L SER 5.4 7.7 + - - +
138L SER* 5.4 0.2 - - - -
222L LYS* 5.4 10.1 - - + -
223L GLY* 1.3 83.0 - - - +
225L TRP* 1.3 62.4 + - - +
274L PHE* 3.4 6.6 - - - +
275L LYS* 2.8 64.5 + - + +
378L GLU* 3.7 25.8 - - + +
379L GLY 4.7 0.4 - - - +
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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