Contacts of the strand formed by residues 205 - 217 (chain A) in PDB entry 3HCE
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A PRO* 4.3 1.3 - - - -
175A ALA 4.0 4.0 - - - +
177A ALA* 3.6 31.0 - - - -
178A LEU* 3.5 23.1 - - + -
201A ILE 3.7 0.8 + - - -
202A THR 3.4 8.5 + - - +
203A THR 3.3 1.8 - - - +
204A LEU* 1.3 78.7 - - - +
206A ARG* 1.3 71.2 + - - +
207A PRO* 4.0 1.2 - - - +
209A GLY* 3.8 13.0 - - - +
210A HIS 3.6 20.0 - - - +
211A LEU 4.5 0.2 - - - +
248A TYR* 3.3 37.0 - - + +
279A LYS* 2.8 44.1 + - + -
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER 4.7 8.3 + - - -
174A PRO* 3.5 25.3 - - + +
175A ALA 3.0 21.1 + - - +
176A ASP* 3.6 39.7 + - - +
204A LEU 3.6 2.6 + - - -
205A LEU* 1.3 80.1 - - - +
207A PRO* 1.3 83.8 + - + +
208A GLY* 3.1 32.6 + - - -
209A GLY* 3.0 21.3 + - - +
210A HIS* 5.8 2.6 - - - -
279A LYS* 3.6 1.9 - - - +
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Residues in contact with PRO 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PRO* 5.2 4.3 - - + -
205A LEU 3.5 3.8 - - - +
206A ARG* 1.3 107.6 + - + +
208A GLY* 1.3 58.4 + - - +
209A GLY 3.3 0.4 - - - -
279A LYS* 4.1 18.6 - - + +
280A VAL 4.3 11.9 - - - +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ARG* 3.1 21.7 + - - -
207A PRO* 1.3 70.8 - - - +
209A GLY* 1.3 64.6 + - - +
210A HIS* 4.1 4.7 + - - -
278A GLN* 3.5 22.9 + - - -
279A LYS 2.8 24.0 + - - -
280A VAL 4.5 2.3 - - - -
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Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASP 3.5 16.4 - - - -
205A LEU* 3.8 8.2 - - - +
206A ARG* 3.0 25.6 + - - +
207A PRO 3.3 1.4 + - - -
208A GLY* 1.3 81.1 - - - +
210A HIS* 1.3 63.3 + - - -
278A GLN* 3.5 4.2 - - - +
279A LYS* 3.1 24.3 + - - +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 3.0 29.0 + - + -
70A VAL* 3.9 24.0 - - + -
71A SER 4.8 4.7 - - - -
176A ASP 3.5 8.8 + - - -
177A ALA* 3.1 7.1 - - + +
178A LEU 2.8 26.5 + - - +
205A LEU* 3.6 5.1 - - - +
206A ARG* 5.8 2.5 - - - -
208A GLY 4.1 3.7 + - - -
209A GLY* 1.3 79.9 - - - -
211A LEU* 1.3 61.2 + - - +
212A LEU* 4.1 2.2 - - + -
251A ARG* 4.0 4.3 - - - -
276A TRP* 2.9 40.1 + + + +
277A ALA 3.4 2.5 - - - +
278A GLN* 3.5 39.7 + - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 6.0 0.2 - - + -
178A LEU* 3.4 32.5 - - + +
179A VAL* 4.5 1.8 - - - +
180A SER* 4.9 3.6 - - - +
198A LEU* 4.3 13.2 - - + -
201A ILE* 4.8 9.4 - - + -
205A LEU* 4.5 2.0 - - + +
209A GLY 4.3 0.2 + - - -
210A HIS* 1.3 74.1 - - - +
212A LEU* 1.3 72.6 + - - +
213A LEU* 4.2 20.4 - - + -
243A LEU* 4.0 23.1 - - + -
248A TYR* 3.8 32.5 - - + +
275A ALA 3.2 3.8 - - - +
277A ALA* 2.6 45.8 + - + +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 3.9 26.7 - - + -
64A THR* 4.0 19.5 - - + -
65A PHE* 3.9 24.9 - - + -
70A VAL* 5.1 8.3 - - + -
178A LEU 2.8 14.2 + - - +
179A VAL* 3.2 13.2 - - + +
180A SER 2.9 26.2 + - - +
210A HIS* 5.2 1.3 - - + -
211A LEU* 1.3 80.9 - - - +
213A LEU* 1.3 59.5 + - - +
214A ILE* 5.4 1.8 - - - +
274A PHE* 4.4 11.9 - - + -
275A ALA 3.4 2.0 - - - +
276A TRP* 3.5 35.2 - - + -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A SER* 3.4 32.1 - - - +
183A CYS 6.2 0.4 - - - +
184A LEU* 4.7 19.7 - - + +
185A ASP* 5.7 2.2 - - - +
194A PHE* 5.0 11.0 - - + -
198A LEU* 5.3 4.5 - - + -
201A ILE* 5.5 1.3 - - + -
211A LEU* 4.2 20.4 - - + -
212A LEU* 1.3 74.3 - - - +
214A ILE* 1.3 66.6 + - - +
239A VAL* 4.8 8.1 - - + -
243A LEU* 4.3 21.5 - - + -
273A PHE* 3.9 25.0 - - + -
274A PHE* 3.4 2.8 - - - -
275A ALA* 2.6 50.6 + - + +
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TRP* 5.9 0.4 - - + -
57A LYS* 4.3 19.7 - - + -
61A LEU* 4.1 31.0 - - + -
85A TYR* 4.9 2.5 - - + -
86A GLN* 5.4 1.8 - - + -
179A VAL* 6.3 2.0 - - + -
180A SER 2.8 7.8 + - - +
181A ALA* 3.0 18.8 - - + -
182A PHE* 2.7 52.2 + - + -
185A ASP* 4.2 1.7 - - - +
212A LEU 5.4 1.3 - - - +
213A LEU* 1.3 78.7 - - - +
215A GLY* 1.3 62.0 + - - +
272A VAL* 4.2 7.9 - - + -
273A PHE* 3.3 17.3 - - - +
274A PHE* 3.6 26.0 - - + -
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Residues in contact with GLY 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PHE* 3.5 13.7 - - - -
185A ASP* 3.7 11.4 - - - -
214A ILE* 1.3 76.0 - - - +
216A ALA* 1.3 60.1 + - - -
272A VAL* 3.5 9.0 - - - +
273A PHE* 2.9 48.1 + - - -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PHE* 3.7 8.2 - - + -
185A ASP* 3.0 20.5 + - + +
215A GLY* 1.3 73.0 - - - -
217A LEU* 1.3 60.2 + - - +
218A GLU 4.1 0.4 + - - -
219A GLU* 3.6 37.9 + - + +
231A VAL* 5.9 1.3 - - + -
234A VAL* 3.2 24.1 + - - +
269A VAL* 4.2 7.0 - - + -
271A GLY 4.0 3.8 - - - -
273A PHE* 3.6 3.3 - - - -
291A OTR 4.4 7.4 - - - +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA* 1.3 72.5 - - - +
218A GLU* 1.3 75.9 + - + +
219A GLU 3.1 2.0 + - - -
234A VAL* 3.5 12.6 - - + +
235A SER* 4.0 18.4 - - - +
236A GLU* 4.0 8.1 - - + +
255A THR* 3.4 39.9 - - + +
269A VAL* 4.0 0.5 - - - +
270A LYS* 3.1 20.4 + - + +
271A GLY* 3.0 24.3 + - - +
272A VAL 4.2 9.2 - - - +
273A PHE* 3.4 33.9 - - + -
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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