Contacts of the strand formed by residues 199 - 205 (chain A) in PDB entry 1IAX
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 VAL 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ALA* 3.4 8.1 - - + +
146A LEU* 3.9 24.9 - - + +
168A ILE* 4.3 12.3 - - + -
189A TYR* 4.2 23.2 - - + +
192A ALA* 4.0 27.1 - - + -
193A GLN* 5.7 1.5 - - + +
197A ILE 3.1 5.4 + - - +
198A LYS* 1.3 74.2 - - - +
200A LYS* 1.3 59.5 + - - +
201A GLY 3.4 28.0 - - - +
232A ILE* 3.2 26.2 - - + +
11B ILE* 5.4 2.1 - - - +
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Residues in contact with LYS 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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138A LEU 3.9 15.0 + - - +
139A ALA* 3.9 18.4 - - + +
140A ASP* 3.6 18.8 + - - +
143A ASP* 3.0 49.4 - - + +
144A ALA 2.9 8.1 + - - +
145A PHE* 4.2 4.0 - - + -
198A LYS* 2.7 41.3 - - + +
199A VAL* 1.3 74.5 - - - +
201A GLY* 1.3 57.2 + - - +
231A ASN 4.7 0.5 - - - +
232A ILE* 3.4 8.0 - - - -
233A HIS* 2.9 29.6 + - - +
11B ILE* 3.9 25.5 - - + +
12B LEU 5.1 5.1 + - - -
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Residues in contact with GLY 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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144A ALA 3.8 2.4 + - - -
145A PHE* 3.1 22.6 - - - -
146A LEU 2.8 27.9 + - - -
199A VAL* 3.4 12.4 - - - +
200A LYS* 1.3 81.9 - - - +
202A LEU* 1.3 53.9 + - - +
232A ILE* 3.8 6.7 - - - -
233A HIS 3.1 15.5 - - - -
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Residues in contact with LEU 202 (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 PHE* 3.7 2.6 - - - -
146A LEU* 3.3 31.0 - - + +
148A PRO* 4.4 4.5 - - + -
170A ILE* 4.4 6.5 - - + -
180A ILE* 6.3 0.4 - - + -
185A VAL* 3.9 29.2 - - + -
201A GLY* 1.3 74.8 - - - +
203A ILE* 1.3 66.4 - - - +
204A LEU* 3.8 32.5 - - + -
223A VAL* 3.9 17.7 - - + -
226A PHE* 5.2 2.7 - - + -
227A THR* 4.3 12.8 - - - +
232A ILE* 5.0 2.9 - - + -
233A HIS 2.7 12.0 + - - +
234A LEU* 3.4 9.1 - - + +
235A VAL 3.0 21.3 + - - -
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Residues in contact with ILE 203 (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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131A ASN* 4.1 15.5 - - - +
134A ILE* 5.5 1.1 - - + -
135A ILE* 5.4 4.0 - - + -
145A PHE* 3.9 17.5 - - + -
146A LEU 2.9 14.6 + - - +
147A VAL* 3.9 21.1 - - + +
148A PRO* 3.4 17.8 - - - +
155A PHE* 3.9 25.5 - - + -
159A LEU* 4.2 23.6 - - + -
202A LEU* 1.3 76.8 - - - +
204A LEU* 1.3 67.6 + - - +
205A THR* 5.0 1.2 + - - -
235A VAL* 3.3 28.5 - - + +
237A ASP* 4.5 3.4 - - + +
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Residues in contact with LEU 204 (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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148A PRO* 3.7 13.5 - - + -
180A ILE* 3.5 32.8 - - + -
202A LEU* 3.8 15.7 - - + +
203A ILE* 1.3 76.7 - - - +
205A THR* 1.3 68.0 + - - +
206A ASN* 5.0 1.8 - - + +
215A LEU* 3.9 23.1 - - + -
220A LEU* 4.0 17.5 - - + -
223A VAL* 3.9 27.8 - - + -
234A LEU* 4.1 9.0 - - + -
235A VAL 2.9 11.6 + - - +
236A CYS* 4.6 9.2 - - - -
237A ASP* 2.9 28.7 + - - +
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Residues in contact with THR 205 (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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148A PRO* 5.7 0.2 - - - +
151A TYR* 5.9 0.9 - - - +
152A TYR* 5.4 1.8 + - + +
155A PHE* 3.8 25.8 - - - -
203A ILE 5.0 0.5 + - - -
204A LEU* 1.3 78.2 + - - +
206A ASN* 1.3 62.0 + - - +
207A PRO 3.2 16.6 - - - +
208A SER* 3.6 13.7 + - - -
209A ASN* 3.9 22.8 + - + +
215A LEU* 4.5 6.4 - - - +
237A ASP* 3.4 11.7 - - + +
239A ILE* 5.1 0.2 - - + -
240A TYR* 4.8 4.0 - - + -
500A PLP 3.8 24.4 - - + +
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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