Contacts of the strand formed by residues 191 - 201 (chain A) in PDB entry 3IAY
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A VAL* 4.0 20.4 - - + +
183A LEU* 3.6 35.4 - - + +
184A ASN* 2.7 43.2 + - - +
187A PHE* 3.5 36.3 - - + +
189A HIS 3.5 0.5 - - - +
190A ALA* 1.3 76.2 - - - +
192A ASP* 1.3 64.0 + - - +
193A SER 4.1 5.6 - - - +
216A ILE* 4.0 15.3 - - + -
217A TYR 3.7 8.5 - - - +
218A VAL* 4.6 2.2 - - + -
219A THR* 4.9 1.3 - - - -
223A MET* 4.9 2.9 - - + -
227A LEU* 4.2 21.5 - - + -
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Residues in contact with ASP 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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132A ASN* 2.7 41.0 + - - +
157A LYS* 3.5 35.2 + - + -
180A VAL* 4.5 6.3 - - - +
190A ALA 3.7 2.8 + - - -
191A ILE* 1.3 75.5 - - - +
193A SER* 1.3 84.4 + - - +
217A TYR* 2.8 19.3 + - + +
219A THR* 4.4 6.5 - - + +
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Residues in contact with SER 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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157A LYS* 5.0 0.2 - - - -
180A VAL* 4.5 10.1 - - - -
191A ILE* 3.7 2.9 - - - +
192A ASP* 1.3 101.2 + - - +
194A ILE* 1.3 68.1 + - - +
215A LYS 3.8 0.3 - - - +
216A ILE* 3.6 3.8 - - - +
217A TYR* 3.0 40.9 + - - +
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Residues in contact with ILE 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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173A GLN* 5.4 3.8 + - - -
176A ILE* 4.0 23.4 - - + +
179A PHE* 3.7 29.6 - - + -
180A VAL* 3.7 24.7 - - + +
183A LEU* 4.7 2.9 - - + -
193A SER* 1.3 85.1 - - - +
195A GLU* 1.3 64.4 + - - +
196A VAL* 4.2 4.4 + - + +
214A TRP* 3.8 44.0 - - + -
215A LYS 3.3 5.4 - - - +
216A ILE* 3.8 22.0 - - + -
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Residues in contact with GLU 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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193A SER 4.2 0.2 - - - -
194A ILE* 1.3 74.8 - - - +
196A VAL* 1.3 67.8 + - - +
197A VAL* 3.6 20.2 + - + +
213A PHE 3.7 0.2 - - - +
214A TRP* 3.7 1.4 - - - -
215A LYS* 2.8 41.5 + - + +
217A TYR* 2.5 43.6 + - + -
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Residues in contact with VAL 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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164A ALA* 5.7 0.2 - - + -
170A ALA 5.8 0.2 - - - +
173A GLN* 6.0 1.1 - - - +
176A ILE* 4.4 17.7 - - + -
194A ILE* 5.2 4.3 - - + +
195A GLU* 1.3 79.9 - - - +
197A VAL* 1.3 70.4 + - - +
212A PRO* 4.6 13.9 - - + -
213A PHE 3.6 8.7 - - - +
214A TRP* 3.9 23.8 - - + +
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Residues in contact with VAL 197 (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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161A TYR* 3.7 27.8 - - + +
195A GLU* 4.0 28.9 - - + +
196A VAL* 1.3 82.1 - - - +
198A SER* 1.3 58.8 + - - +
199A LYS* 3.8 21.1 - - + -
211A LEU 3.5 0.2 - - - +
212A PRO* 3.4 4.7 - - - +
213A PHE* 2.7 51.3 + - + +
215A LYS* 4.5 11.7 - - + -
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Residues in contact with SER 198 (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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197A VAL* 1.3 73.2 - - - +
199A LYS* 1.3 73.1 + - - +
210A LYS* 3.5 35.1 + - - +
211A LEU 3.3 11.5 + - - -
212A PRO* 5.0 1.7 - - - +
572A ASP* 4.0 5.7 - - - +
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Residues in contact with LYS 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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161A TYR* 3.6 32.2 + - + -
197A VAL* 3.8 24.2 + - + -
198A SER* 1.3 83.0 - - - +
200A GLN* 1.3 61.1 + - - +
210A LYS* 3.5 5.7 - - - +
211A LEU* 2.8 33.1 + - - +
213A PHE* 3.6 24.7 - - + -
569A LEU* 4.6 15.8 - - - +
572A ASP* 3.3 40.4 + - - +
573A THR 5.0 1.0 + - - +
574A VAL* 4.1 24.1 - - + +
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Residues in contact with GLN 200 (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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199A LYS* 1.3 75.7 - - - +
201A SER* 1.3 70.3 + - - +
207A GLY 4.1 9.9 + - - -
208A ASP* 4.2 9.3 + - - +
209A THR 4.5 4.2 + - - +
210A LYS* 4.0 25.8 - - + +
211A LEU* 5.9 2.7 - - + -
213A PHE* 4.7 2.5 - - - -
571A ILE* 3.7 12.1 - - - +
572A ASP 3.0 8.6 + - - +
573A THR* 3.1 25.4 + - - +
574A VAL* 2.8 28.1 + - - -
659A ARG* 3.9 29.0 + - - +
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Residues in contact with SER 201 (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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200A GLN* 1.3 82.0 - - - +
202A ILE* 1.3 65.6 + - - +
203A TRP* 3.0 26.3 + - - +
204A GLY 4.4 8.1 - - - +
213A PHE* 4.7 6.4 - - - -
249A TYR* 3.6 29.4 + - - -
573A THR* 3.9 2.0 - - - +
574A VAL* 3.4 10.2 - - - +
576A PRO* 3.9 5.2 - - - +
625A THR* 5.5 0.5 - - - +
659A ARG* 5.3 2.8 + - - -
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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