Contacts of the strand formed by residues 152 - 159 (chain T) in PDB entry 4IBL
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 152 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144T ARG* 4.0 0.9 - - - +
149T LYS 4.9 4.7 - - - +
150T ASP 4.1 0.4 + - - -
151T LEU* 1.3 84.6 - - - +
153T TYR* 1.3 66.8 + - - +
154T THR* 3.7 23.6 - - + -
169T LYS* 4.2 21.5 - - + +
170T THR 3.3 13.2 - - - +
171T ASN* 3.7 20.4 - - - +
192T VAL* 2.9 44.1 + - + +
194T PRO* 3.7 33.4 - - + -
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Residues in contact with TYR 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T PRO* 4.3 3.8 - - + -
127T VAL* 3.9 23.3 - - + -
130T GLU* 3.5 22.7 - - - +
143T LEU* 4.0 2.8 - - - +
144T ARG* 3.8 9.0 - - - -
151T LEU* 3.8 24.0 - - + +
152T ILE* 1.3 74.7 - - - +
154T THR* 1.3 63.3 + - - +
169T LYS* 3.4 2.3 - - - +
170T THR* 2.9 37.1 + - + -
172T THR 3.9 8.5 - - - -
173T ASN* 3.5 30.6 + - - -
175T PHE* 3.4 21.6 - - + -
189T VAL* 5.2 0.4 - - + -
190T GLN 3.3 18.2 - - - +
191T ALA* 3.5 22.0 - - + -
301T CL 3.0 21.1 - - - +
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Residues in contact with THR 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152T ILE* 3.7 24.2 - - + -
153T TYR* 1.3 78.3 - - - +
155T LEU* 1.3 58.9 - - - +
156T TYR* 4.8 6.6 - - - -
167T THR* 4.9 5.4 - - - -
168T ALA 3.3 8.3 - - - -
169T LYS* 3.8 22.9 - - + -
175T PHE* 3.6 1.8 - - - -
188T SER 4.0 0.2 - - - +
189T VAL* 3.1 8.7 - - - +
190T GLN* 2.9 51.9 + - - +
192T VAL* 3.7 17.0 - - + +
201T LYS* 5.5 2.3 + - - +
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Residues in contact with LEU 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125T VAL* 4.1 13.9 - - + -
154T THR* 1.3 72.9 - - - +
156T TYR* 1.3 61.1 + - - +
157T TYR* 3.8 22.2 - - + -
166T LYS 3.8 0.2 - - - +
167T THR* 3.1 11.3 - - - +
168T ALA* 2.7 34.0 + - + +
175T PHE* 3.6 31.6 - - + -
177T ILE* 4.0 22.9 - - + -
187T PHE* 3.7 37.2 - - + -
188T SER 3.4 7.9 - - - +
189T VAL* 3.6 22.9 - - + -
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Residues in contact with TYR 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L LEU* 4.6 7.2 - - + -
154T THR* 4.8 9.0 - - - -
155T LEU* 1.3 72.0 - - - +
157T TYR* 1.3 61.1 + - - +
158T TRP* 4.5 4.1 - - + -
165T LYS* 3.3 46.7 - - + +
166T LYS 3.6 2.0 - - - -
167T THR* 3.6 25.0 - - + +
187T PHE* 3.5 1.2 - - - -
188T SER* 2.8 45.2 + - - +
189T VAL 5.9 0.2 - - - -
190T GLN* 3.4 28.2 + - + -
201T LYS* 4.5 11.6 + - - -
204T ASP* 4.2 12.8 - - - -
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Residues in contact with TYR 157 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155T LEU* 3.8 18.4 - - + -
156T TYR* 1.3 74.1 - - - +
158T TRP* 1.3 70.2 + - - +
165T LYS* 3.9 2.5 - - - +
166T LYS* 3.0 82.4 + - + +
167T THR 4.0 15.1 + - - -
168T ALA* 4.0 10.2 - - + +
177T ILE* 3.3 38.0 - - + +
178T ASP 4.5 8.3 + - - -
185T TYR* 4.0 17.5 - + - -
186T CYS 3.2 15.0 - - - +
187T PHE* 3.3 16.8 - + + -
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Residues in contact with TRP 158 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L PHE* 4.1 13.0 - + - -
36L ARG* 3.4 77.2 - - + +
39L LEU* 3.8 30.5 - - + -
156T TYR 4.5 8.5 - - - -
157T TYR* 1.3 90.0 - - - +
159T LYS* 1.3 64.6 + - - +
160T SER* 4.1 5.2 + - - +
164T GLY 4.1 6.7 - - - +
165T LYS* 4.2 18.2 - - + -
166T LYS* 5.1 3.8 - - - +
185T TYR* 3.1 13.3 - - - -
186T CYS* 3.1 60.7 + - + +
188T SER* 5.3 1.3 - - - -
207T VAL* 4.0 21.5 - - + -
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Residues in contact with LYS 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ARG* 3.2 13.9 + - - +
158T TRP* 1.3 73.6 - - - +
160T SER* 1.3 69.3 + - - +
161T SER* 3.6 12.5 + - - +
162T SER* 3.3 32.8 + - - +
164T GLY 5.3 0.6 + - - -
166T LYS* 4.9 13.9 - - - +
180T ASP* 3.3 20.8 + - - +
183T GLU* 2.9 43.6 + - + +
184T ASN 3.5 9.6 - - - +
185T TYR* 3.7 35.0 - - + +
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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