Contacts of the strand formed by residues 152 - 157 (chain B) in PDB entry 5I2Y
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 SER 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 4.5 4.0 - - - -
145B LEU* 3.7 25.3 - - - +
146B VAL 3.1 12.8 - - - -
151B HIS* 1.3 73.7 - - - +
153B VAL* 1.3 65.0 - - - +
221B VAL* 3.9 17.1 + - - -
222B PRO 3.0 6.8 + - - -
223B GLY* 3.4 17.7 + - - -
224B CYS* 3.1 28.8 + - - +
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 5.7 0.4 - - + -
99B ILE* 3.2 47.1 - - + -
103B ILE* 5.3 2.5 - - + -
145B LEU* 3.5 7.8 - - - -
146B VAL* 3.0 31.2 + - + +
152B SER* 1.3 77.1 - - - +
154B ARG* 1.3 77.6 + - - +
155B CYS* 3.5 6.8 + - - -
202B PHE 4.3 6.3 - - - +
203B TYR* 3.9 18.6 - - - -
204B LEU* 3.9 21.8 - - + +
224B CYS* 3.8 8.1 - - - -
225B ASN* 6.1 0.2 - - - +
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Residues in contact with ARG 154 (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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121B LEU* 4.0 26.7 - - + -
143B THR* 4.5 16.9 - - + +
144B LEU 3.3 7.6 - - - +
145B LEU* 4.1 10.1 - - + +
153B VAL* 1.3 76.9 - - - +
155B CYS* 1.3 58.3 + - - +
156B LEU 4.1 0.2 - - - -
192B GLN* 3.3 44.3 + - - +
201B GLU* 3.1 32.0 + - - +
202B PHE 5.3 1.6 + - - +
203B TYR* 3.3 27.0 - - + +
204B LEU 3.1 22.7 + - - -
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Residues in contact with CYS 155 (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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142B ALA 3.6 0.2 - - - +
143B THR* 3.4 5.1 - - - -
144B LEU* 2.7 44.6 + - + +
146B VAL* 3.6 35.9 - - + -
153B VAL* 4.1 4.5 - - - -
154B ARG* 1.3 75.4 - - - +
156B LEU* 1.3 62.1 + - - +
157B VAL* 3.5 5.3 + - + +
184B LEU* 4.0 20.2 - - + -
204B LEU* 3.5 21.8 - - - -
206B VAL* 3.8 16.4 - - + -
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Residues in contact with LEU 156 (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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140B VAL* 5.4 8.1 - - + -
141B GLY* 4.7 7.9 - - - +
142B ALA 3.2 24.2 - - - +
143B THR* 4.3 11.9 - - + +
154B ARG 4.1 0.8 - - - -
155B CYS* 1.3 71.0 - - - +
157B VAL* 1.3 68.2 + - - +
158B THR* 3.6 9.5 + - + +
203B TYR* 4.2 25.9 - - + +
204B LEU 2.8 15.1 + - - +
205B GLN* 3.4 11.3 - - + +
206B VAL 2.8 25.5 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY* 3.4 2.9 - - - -
142B ALA* 2.7 41.9 + - + +
144B LEU* 3.8 33.7 - - + -
155B CYS* 4.3 3.6 - - + +
156B LEU* 1.3 74.3 - - - +
158B THR* 1.3 64.5 + - - +
161B ALA* 3.8 11.9 - - + -
162B LEU* 4.3 9.4 - - + +
174B PHE* 4.5 8.5 - - + -
182B LEU* 5.9 0.2 - - + -
184B LEU* 5.9 2.0 - - + -
206B VAL* 3.6 20.9 - - + +
209B PHE* 3.8 32.8 - - + -
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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