Contacts of the strand formed by residues 166 - 170 (chain B) 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 GLN 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B GLY* 2.6 29.5 + - - -
143B ASP 2.9 13.3 + - - +
144B ALA* 3.3 11.1 - - + -
145B PHE 2.8 24.9 + - - -
160B ARG* 4.1 6.3 - - - +
164B GLY 4.9 2.5 - - - +
165B VAL* 1.3 80.3 - - - +
167B LEU* 1.3 71.6 + - - +
168B ILE* 5.5 1.8 - - - +
197B ILE* 3.7 25.6 - - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PHE* 3.4 12.6 - - + +
147B VAL* 3.6 24.2 - - + -
151B TYR* 3.8 30.7 - - + +
155B PHE* 4.1 17.7 - - + +
156B ASN* 3.9 7.0 - - - +
159B LEU* 4.0 19.3 - - + -
160B ARG* 3.3 36.3 - - + +
165B VAL* 5.3 1.3 - - + -
166B GLN* 1.3 83.9 - - - +
168B ILE* 1.3 70.4 + - - +
169B PRO* 4.1 5.5 - - + +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA* 3.5 26.7 - - + -
145B PHE 2.9 9.4 + - - +
146B LEU* 3.2 24.7 - - + +
147B VAL* 3.0 21.7 + - - -
166B GLN* 5.3 2.9 - - + +
167B LEU* 1.3 80.5 - - - +
169B PRO* 1.3 74.1 - - + +
188B ALA* 4.4 12.8 - - + +
192B ALA* 3.9 25.4 - - + -
197B ILE* 4.0 18.4 - - + -
199B VAL* 4.7 3.8 - - + -
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 3.2 11.0 - - + +
149B SER* 4.4 17.3 - - - +
151B TYR* 4.8 10.5 - - + +
167B LEU* 4.1 6.2 - - + +
168B ILE* 1.3 92.9 - - + +
170B ILE* 1.3 60.2 + - - +
171B HIS 4.0 1.3 + - - -
188B ALA* 3.6 15.2 - - - +
404B GLU* 5.9 2.5 - - + -
406B GLN* 4.7 10.5 - - - +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 4.0 18.6 - - + -
147B VAL 2.9 8.8 + - - +
148B PRO* 3.6 25.0 - - + +
149B SER* 3.1 23.2 + - - -
169B PRO* 1.3 74.3 - - - +
171B HIS* 1.3 75.5 + - - +
172B CYS* 3.7 0.9 - - - -
180B ILE* 4.6 8.3 - - + -
184B ALA* 4.0 22.2 - - + +
185B VAL* 4.1 23.3 - - + +
188B ALA* 4.0 18.8 - - + -
202B LEU* 3.8 29.2 - - + -
406B GLN* 4.7 0.2 - - - -
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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