Contacts of the strand formed by residues 155 - 159 (chain G) in PDB entry 1I43
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 HIS 155 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150G VAL* 4.7 1.1 - - - +
154G GLY* 1.3 74.1 - - - -
156G ILE* 1.3 74.8 + - - +
157G VAL* 4.3 10.8 - - + -
179G ILE* 5.0 0.9 - - - -
180G THR* 3.0 42.7 + - + +
181G ALA 3.5 12.6 - - - -
182G THR* 2.6 33.9 + - - -
195G ALA* 5.5 0.7 - - + -
199G LYS* 3.7 37.9 - - + +
200G LYS 3.8 18.0 + - - +
201G VAL* 4.4 6.7 - - + -
202G ASN* 2.9 37.6 + - - +
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Residues in contact with ILE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G LEU* 3.4 33.7 - - + -
150G VAL* 4.1 11.2 - - + -
155G HIS* 1.3 77.5 - - - +
157G VAL* 1.3 62.5 + - - +
158G THR* 4.5 17.3 - - + -
170G ILE* 4.2 13.5 - - + -
174G LEU* 4.8 8.5 - - + -
179G ILE* 4.6 8.3 - - + -
180G THR 2.8 8.3 + - - +
181G ALA* 3.1 25.1 - - + -
182G THR 2.7 32.2 + - - -
203G LEU* 3.3 33.2 - - + +
205G PHE* 4.8 0.7 - - + -
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Residues in contact with VAL 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G HIS* 4.3 5.4 - - + -
156G ILE* 1.3 80.2 - - - +
158G THR* 1.3 65.9 + - - +
182G THR* 3.4 21.1 - - + +
184G ILE* 4.4 8.7 - - + -
192G LEU* 3.8 16.6 - - + -
195G ALA* 4.6 7.0 - - + -
196G LEU* 5.9 0.2 - - + -
201G VAL* 3.4 40.2 - - + -
203G LEU 3.1 6.6 + - - +
204G PHE* 3.0 27.1 - - + -
205G PHE 2.8 31.9 + - - -
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Residues in contact with THR 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G ILE* 4.5 12.9 - - + +
157G VAL* 1.3 78.7 - - - +
159G THR* 1.3 69.6 + - - +
162G CYS* 4.4 10.9 - - - +
167G ARG* 5.9 1.2 - - - -
170G ILE* 4.4 18.7 - - + +
181G ALA* 5.4 1.7 - - - +
182G THR 3.1 4.9 + - - +
183G VAL* 3.3 18.2 - - - +
184G ILE* 2.9 26.3 + - - +
204G PHE* 4.2 6.3 - - - -
205G PHE* 3.0 43.3 - - + +
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Residues in contact with THR 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G THR* 1.3 83.1 + - - +
160G THR* 1.3 62.5 + - - +
161G ASP* 3.3 14.2 + - - +
162G CYS* 3.5 25.0 + - - +
167G ARG* 5.0 2.3 + - - -
183G VAL* 3.6 8.9 - - - +
184G ILE* 3.0 13.2 - - + +
185G ASP 4.9 0.9 - - - +
186G PRO* 3.9 30.6 - - + +
204G PHE* 4.4 10.8 - - + -
205G PHE 4.1 0.4 + - - -
206G THR* 3.0 34.5 + - - +
207G GLU* 5.7 0.3 - - - +
210G THR* 4.4 2.8 + - - -
217G VAL* 4.8 2.5 - - + -
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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