Contacts of the strand formed by residues 190 - 199 (chain A) in PDB entry 6DWW
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 ASN 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A LEU* 5.2 4.3 - - + -
182A TRP 3.4 6.5 - - - +
183A THR* 4.1 14.8 - - + +
188A LYS 4.6 4.2 + - - -
189A ARG* 1.3 75.8 - - - +
191A PHE* 1.3 60.0 + - - +
213A SER* 3.4 5.7 - - - -
214A LEU* 2.9 36.8 + - + +
216A PHE* 3.9 27.3 + - - +
217A GLU 4.1 7.1 - - - +
219A SER* 4.2 21.4 + - - +
20C T 6.0 4.0 - - - -
21C C 5.9 0.8 + - - -
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Residues in contact with PHE 191 (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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181A LEU* 3.2 16.2 - - - +
182A TRP* 2.5 61.3 + + + +
184A ASP* 4.0 8.5 - - + -
189A ARG* 3.5 60.8 - - + -
190A ASN* 1.3 73.4 - - - +
192A LEU* 1.3 58.9 + - - +
193A GLY 4.0 0.2 - - - -
211A LEU* 3.4 54.7 - - + -
212A LYS 3.7 2.2 - - - -
213A SER* 3.7 19.7 - - - -
214A LEU* 4.3 1.6 - - - -
582A ILE* 4.8 4.9 - - + -
591A GLN* 4.8 14.1 - - + -
594A VAL* 5.8 3.4 - - + -
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Residues in contact with LEU 192 (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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179A ILE* 4.1 14.8 - - + -
180A ASP 3.3 18.8 - - - +
181A LEU* 4.7 5.6 - - + -
191A PHE* 1.3 73.4 - - - +
193A GLY* 1.3 66.3 + - - +
194A VAL* 4.2 11.7 - - + -
210A GLY 3.4 5.9 - - - +
211A LEU* 3.5 3.0 - - - -
212A LYS 3.0 33.0 + - - +
214A LEU* 4.1 12.3 - - + +
224A ILE* 3.6 42.4 - - + +
227A LYS* 3.8 13.5 - - + +
228A LEU* 3.7 23.8 - - + +
231A ILE* 4.0 4.9 - - + +
253A VAL* 6.2 0.9 - - + -
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Residues in contact with GLY 193 (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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178A THR 4.3 0.9 - - - -
179A ILE* 3.1 30.4 - - - +
180A ASP 3.1 12.2 + - - -
192A LEU* 1.3 74.5 - - - +
194A VAL* 1.3 60.6 + - - +
195A THR* 5.6 0.2 - - - -
210A GLY 3.6 5.4 - - - -
211A LEU* 3.9 13.0 - - - -
571A SER* 4.5 5.8 - - - -
574A THR* 5.3 5.2 - - - -
575A PHE* 4.0 15.6 - - - -
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Residues in contact with VAL 194 (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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177A ALA* 4.8 1.1 - - + -
178A THR 3.5 3.1 - - - -
179A ILE* 3.7 20.9 - - + -
192A LEU* 4.2 7.2 - - + -
193A GLY* 1.3 79.3 - - - +
195A THR* 1.3 75.1 + - - +
208A ILE* 3.8 2.4 - - - +
209A LEU* 2.9 32.4 + - + -
210A GLY 3.1 13.2 + - - +
228A LEU* 3.7 13.0 - - + -
231A ILE* 3.7 30.5 - - + -
232A PHE* 4.0 27.6 - - + -
574A THR* 5.8 1.2 - - - +
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Residues in contact with THR 195 (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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177A ALA* 3.1 29.3 - - - +
178A THR* 2.7 29.4 + - - +
194A VAL* 1.3 80.6 - - - +
196A LEU* 1.3 61.9 + - - +
197A HIS* 2.8 22.1 + - - -
206A ASP* 4.6 2.2 - - - +
207A LEU 3.1 13.7 - - - +
208A ILE* 4.4 7.4 - - + -
209A LEU* 4.3 2.9 - - - +
570A ALA* 3.7 19.4 - - + +
571A SER* 4.2 4.0 - - - +
574A THR* 3.5 24.9 - - - +
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Residues in contact with LEU 196 (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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166A ILE* 3.7 42.8 - - + +
170A VAL* 5.1 5.4 - - + -
175A ALA* 4.4 15.7 - - + -
176A SER 3.4 17.5 - - - +
177A ALA* 4.2 8.3 - - + -
195A THR* 1.3 74.4 - - - +
197A HIS* 1.3 70.6 + - - +
198A TYR* 3.9 20.2 - - + -
205A ARG* 3.6 3.6 - - - +
206A ASP* 3.6 0.2 - - - -
207A LEU* 2.8 39.3 + - + +
209A LEU* 3.7 29.8 - - + -
232A PHE* 4.3 9.6 - - + -
243A ILE* 4.5 3.8 - - + -
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Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLY 4.0 0.3 - - - +
175A ALA* 3.7 1.0 - - - -
176A SER* 2.8 52.7 + - - +
177A ALA* 4.2 5.4 - - - -
178A THR* 4.0 2.5 - - + +
195A THR* 2.8 26.8 + - - -
196A LEU* 1.3 82.6 + - - +
198A TYR* 1.3 63.5 + - - +
204A LEU* 6.1 1.1 - - + -
205A ARG 3.4 12.4 + - - +
206A ASP* 3.3 29.5 + - - -
377A CYS* 4.0 11.0 + - - +
563A SER* 3.5 15.8 + - - +
565A PRO* 3.6 26.9 - - + +
570A ALA* 3.7 17.3 - - + +
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Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 4.7 10.8 + - - +
166A ILE* 3.7 27.3 - - + +
169A ALA* 3.9 27.4 - - + -
174A GLY 3.2 22.4 - - - +
175A ALA* 4.4 1.8 - - + -
196A LEU* 3.9 18.6 - - + -
197A HIS* 1.3 72.3 - - - +
199A HIS* 1.3 71.6 + - - +
200A GLU* 4.1 17.9 + - - -
204A LEU* 3.7 3.2 - - - +
205A ARG* 2.9 59.7 + - + +
207A LEU* 3.9 8.8 - - + +
563A SER* 4.0 11.8 - - - -
607A PHE* 3.7 19.6 - - - -
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Residues in contact with HIS 199 (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 GLY 4.4 2.2 + - - -
198A TYR* 1.3 86.6 - - - +
200A GLU* 1.3 76.8 + - - +
202A ASN* 3.2 36.1 - - - -
203A GLU 3.3 12.5 + - - -
204A LEU* 4.2 7.9 - - + -
541A MET* 3.5 21.0 - - + +
545A ASN* 3.1 26.8 + - - -
559A LEU* 3.5 41.2 - - + +
563A SER* 4.0 3.8 + - - -
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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