Contacts of the strand formed by residues 212 - 228 (chain A) in PDB entry 5UV6
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 ASP 212 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 3.6 21.0 - - - +
137A GLN* 3.4 14.9 - - - +
138A ILE* 2.7 41.9 + - + +
202A CYS 3.7 1.4 - - - +
203A SER* 3.4 2.4 - - - -
204A ALA* 2.9 32.0 + - - +
210A ALA 3.8 1.0 + - - -
211A PRO* 1.3 73.0 - - - +
213A VAL* 1.3 75.4 + - - +
214A ARG* 6.0 0.2 - - - -
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 4.8 0.9 - - - -
201A GLU* 4.4 21.5 - - + +
202A CYS 3.1 6.3 - - - +
203A SER* 3.8 22.4 - - - +
211A PRO* 3.9 11.2 + - + +
212A ASP* 1.3 90.6 + - - +
214A ARG* 1.3 73.2 + - - +
215A LYS* 6.4 0.4 - - - +
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Residues in contact with ARG 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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138A ILE* 4.7 21.3 - - + +
141A ILE* 4.3 26.4 - - + +
169A TRP* 5.2 0.5 - - - -
201A GLU* 3.7 3.7 - - - -
202A CYS* 2.8 35.8 + - + +
213A VAL* 1.3 81.2 + - - +
215A LYS* 1.3 108.4 + - - +
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Residues in contact with LYS 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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141A ILE* 4.9 6.7 - - - +
142A SER 4.9 1.2 - - - +
144A ASP* 4.7 1.9 - - - +
172A LEU* 3.5 27.4 - - - +
199A GLU* 3.2 32.3 - - + +
200A TYR 3.3 12.1 - - - +
201A GLU* 4.4 14.7 + - - +
213A VAL* 6.4 0.4 - - - +
214A ARG* 1.3 115.4 + - - +
216A VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 4.8 2.7 - - + -
142A SER* 3.3 27.8 - - - +
143A SER 3.7 20.6 - - - +
144A ASP* 3.7 6.1 - - - -
145A ILE* 5.2 0.9 - - + -
155A LEU* 3.7 31.9 - - + -
169A TRP* 3.5 35.9 - - + -
198A GLY 3.8 0.7 - - - +
199A GLU* 3.3 5.2 - - - -
200A TYR* 2.8 29.6 + - - +
215A LYS* 1.3 75.1 - - - +
217A LYS* 1.3 66.3 + - - +
218A ILE 4.0 0.7 + - - -
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Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 2.8 33.4 + - + +
145A ILE* 3.0 28.6 + - - +
198A GLY* 3.5 14.6 - - - +
199A GLU* 4.3 25.4 - - + +
216A VAL* 1.3 73.1 - - - +
218A ILE* 1.3 64.4 + - - +
219A THR* 3.6 26.9 - - + +
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Residues in contact with ILE 218 (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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145A ILE* 3.6 9.9 - - + +
147A VAL* 4.3 13.9 - - + -
153A VAL* 3.7 28.0 - - + -
155A LEU* 3.9 21.3 - - + -
189A ILE* 3.9 12.3 - - + -
192A ILE* 3.6 25.1 - - + -
196A GLN 4.6 1.3 - - - +
197A SER* 3.3 2.4 - - - -
198A GLY* 2.8 37.6 + - - +
200A TYR* 3.5 33.0 - - + -
216A VAL 5.1 0.9 - - - +
217A LYS* 1.3 73.6 - - - +
219A THR* 1.3 63.9 + - - +
220A VAL* 4.2 8.7 - - + -
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Residues in contact with THR 219 (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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145A ILE 2.9 8.6 + - - +
146A THR* 3.0 31.2 - - + +
147A VAL* 2.9 24.8 + - - +
197A SER* 4.3 3.4 - - - -
217A LYS* 3.6 31.2 - - + +
218A ILE* 1.3 77.5 - - - +
220A VAL* 1.3 61.8 + - - +
221A ASN* 3.9 2.3 + - - -
249A VAL* 5.1 9.8 - - - +
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Residues in contact with VAL 220 (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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147A VAL* 3.2 5.8 - - + +
148A ASN 4.2 0.9 - - - -
149A GLU* 3.6 33.9 - - + +
192A ILE* 3.6 39.0 - - + +
193A LYS 3.7 19.1 - - - +
194A ARG* 4.3 6.7 - - + -
197A SER* 3.7 26.3 - - - -
218A ILE* 4.2 2.2 - - + -
219A THR* 1.3 74.6 - - - +
221A ASN* 1.3 67.1 + - - +
222A TYR* 3.5 7.8 - - - -
249A VAL* 3.2 20.7 - - - +
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Residues in contact with ASN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 4.5 19.7 + - - -
147A VAL* 2.8 16.0 + - - +
148A ASN* 3.1 27.6 + - - +
149A GLU* 2.8 31.0 + - - +
219A THR* 3.9 0.7 + - - +
220A VAL* 1.3 71.2 - - - +
222A TYR* 1.3 60.0 + - - +
249A VAL* 3.1 28.8 - - - +
250A PRO* 3.6 12.5 - - - +
302A LEU* 3.9 14.1 - - + +
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Residues in contact with TYR 222 (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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149A GLU* 3.7 8.1 - - + +
194A ARG* 3.5 59.7 - - + +
220A VAL 3.5 12.8 - - - -
221A ASN* 1.3 75.0 - - - +
223A PRO* 1.3 94.3 - - + +
225A TYR* 4.3 3.8 - + - -
247A SER* 3.1 40.3 + - - -
248A ALA* 3.7 13.3 + - - -
249A VAL* 3.0 31.2 + - + +
277A ARG* 4.8 3.5 + - - -
300A ASN* 3.0 17.5 + - - -
302A LEU* 3.9 6.3 - - - +
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Residues in contact with PRO 223 (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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149A GLU* 4.2 6.1 - - + +
194A ARG* 4.1 15.4 + - - +
222A TYR* 1.3 104.3 - - + +
224A PRO* 1.3 79.5 - - + +
225A TYR* 3.8 0.3 + - - +
300A ASN* 3.8 5.4 - - - +
302A LEU* 3.3 33.0 - - + +
303A GLY* 3.8 7.0 - - - -
304A ASN 4.9 0.9 - - - +
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Residues in contact with PRO 224 (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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222A TYR 3.8 0.2 - - - -
223A PRO* 1.3 93.2 - - + +
225A TYR* 1.3 61.8 + - - +
246A ALA* 4.4 2.7 - - + -
247A SER 3.5 8.7 - - - +
248A ALA* 3.5 16.6 - - + -
252A ALA* 4.0 9.4 - - + -
298A ALA* 3.5 35.2 - - + +
299A THR 4.2 1.1 - - - -
300A ASN* 3.4 17.0 - - - +
303A GLY 3.3 24.2 - - - +
304A ASN* 4.2 3.5 - - - +
305A THR* 3.5 14.8 - - + +
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Residues in contact with TYR 225 (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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194A ARG* 3.8 29.8 - - - -
222A TYR* 4.3 4.7 - + - -
224A PRO* 1.3 74.7 - - - +
226A ILE* 1.3 74.8 + - - +
227A SER* 4.0 19.8 - - - -
246A ALA* 3.3 1.5 - - - -
247A SER* 2.8 59.8 + - - -
305A THR* 3.7 8.5 - - - +
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Residues in contact with ILE 226 (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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225A TYR* 1.3 82.1 - - - +
227A SER* 1.3 61.5 + - - +
228A LYS 3.6 21.3 - - - +
229A ALA* 3.9 15.7 - - + -
244A CYS* 4.6 2.5 - - - -
245A GLU 3.7 2.2 - - - +
246A ALA* 4.1 1.8 - - + -
254A PHE* 3.9 31.9 - - + -
296A CYS* 4.4 9.2 - - + +
298A ALA* 4.0 7.6 - - + -
305A THR* 3.8 25.1 + - + +
306A ASN 4.0 20.6 - - - +
307A ALA* 4.0 10.5 - - + +
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Residues in contact with SER 227 (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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225A TYR* 3.4 20.8 + - - -
226A ILE* 1.3 74.0 - - - +
228A LYS* 1.3 57.0 + - - +
245A GLU* 2.6 38.6 + - - +
246A ALA 3.6 10.7 - - - -
247A SER* 4.3 4.9 - - - -
277A ARG* 3.7 8.7 + - - -
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Residues in contact with LYS 228 (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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226A ILE* 3.6 5.3 - - - +
227A SER* 1.3 79.2 - - - +
229A ALA* 1.3 66.4 + - - +
230A LYS* 5.9 6.1 - - + -
243A SER 4.8 0.4 - - - +
244A CYS* 3.3 3.6 - - - -
245A GLU* 2.9 52.8 + - + +
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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