Contacts of the strand formed by residues 155 - 159 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150K VAL* 4.7 1.7 - - - +
154K GLY* 1.3 75.0 - - - -
156K ILE* 1.3 73.1 + - - +
157K VAL* 4.2 10.1 - - + -
180K THR* 2.9 43.9 + - + +
181K ALA 3.4 13.7 - - - -
182K THR* 2.7 34.2 + - - -
195K ALA* 5.7 0.6 - - + +
199K LYS* 3.7 36.8 - - + +
200K LYS 3.7 17.1 + - - +
201K VAL* 4.3 8.3 - - + -
202K ASN* 3.0 37.8 + - - +
203K LEU 3.8 0.2 + - - -
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Residues in contact with ILE 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K LEU* 3.3 33.9 - - + -
150K VAL* 4.1 13.0 - - + -
155K HIS* 1.3 75.5 + - - +
157K VAL* 1.3 68.6 + - - +
158K THR* 4.5 18.2 - - + +
170K ILE* 4.1 15.5 - - + -
174K LEU* 4.8 4.9 - - + -
179K ILE* 4.6 7.6 - - + -
180K THR 2.7 10.5 + - - +
181K ALA* 3.1 25.5 - - + -
182K THR 2.8 25.1 + - - -
203K LEU* 3.4 30.5 - - + +
205K PHE* 4.6 1.3 - - + -
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Residues in contact with VAL 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K HIS* 4.2 5.8 - - + -
156K ILE* 1.3 78.9 - - - +
158K THR* 1.3 69.5 + - - +
182K THR* 3.4 17.3 - - + +
184K ILE* 4.6 12.3 - - + -
192K LEU* 3.8 16.6 - - + -
195K ALA* 4.6 7.2 - - + -
201K VAL* 3.4 36.6 - - + -
203K LEU 3.1 9.6 + - - +
204K PHE* 3.2 26.7 - - + -
205K PHE 2.8 28.1 + - - -
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Residues in contact with THR 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K ILE* 4.3 11.4 - - + +
157K VAL* 1.3 77.9 - - - +
159K THR* 1.3 61.7 + - - +
162K CYS* 4.8 9.8 - - - +
167K ARG* 6.0 1.0 - - - -
170K ILE* 4.3 19.8 - - + +
181K ALA* 5.3 1.9 - - - +
182K THR 3.1 5.0 + - - +
183K VAL* 3.1 21.8 - - - +
184K ILE* 2.8 35.5 + - - +
204K PHE* 4.3 3.6 - - - -
205K PHE* 3.0 44.2 - - + +
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Residues in contact with THR 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K THR* 1.3 80.1 + - - +
160K THR* 1.3 62.7 + - - +
161K ASP* 3.3 16.7 + - - +
162K CYS* 3.4 25.1 + - - +
167K ARG* 5.0 1.7 + - - -
183K VAL* 3.4 10.2 - - - +
184K ILE* 2.8 13.0 - - + +
185K ASP 5.0 0.4 - - - -
186K PRO* 4.0 27.5 - - + +
204K PHE* 4.5 10.1 - - + -
205K PHE 4.2 0.4 + - - -
206K THR* 3.2 34.3 + - - +
207K GLU* 5.6 0.9 - - - +
210K THR* 4.4 3.5 + - - +
217K 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