Contacts of the strand formed by residues 174 - 178 (chain D) in PDB entry 2I5B
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 TYR 174 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D THR* 2.9 22.3 + - + +
137D VAL* 3.3 9.0 - - + -
138D ILE* 3.0 29.3 + - - +
172D ALA* 4.3 0.9 - - - +
173D GLN* 1.3 95.6 - - + +
175D VAL* 1.3 64.7 + - - +
192D LEU* 4.2 19.3 - - + -
193D TYR 3.6 4.0 - - - +
194D ASP* 4.0 28.8 - - + +
232D VAL* 3.6 44.3 - - + +
233D LYS* 4.2 16.8 - - + -
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ILE* 3.6 13.2 - - + +
140D PRO* 4.6 1.6 - - + -
164D ALA* 3.8 15.9 - - + +
167D ILE* 3.6 34.8 - - + -
168D HIS* 3.7 29.8 - - + +
172D ALA* 4.4 2.0 - - + -
174D TYR* 1.3 78.9 - - - +
176D VAL* 1.3 67.6 + - - +
177D ILE* 3.9 25.4 - - + -
191D VAL 3.4 1.1 - - - +
192D LEU* 3.3 5.8 - - - +
193D TYR* 2.9 35.1 + - + +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D VAL* 4.2 8.1 - - + -
138D ILE 2.9 12.4 + - - +
139D THR* 3.2 23.5 - - + -
140D PRO* 3.3 7.4 - - - +
174D TYR 4.2 0.2 - - - -
175D VAL* 1.3 79.6 - - - +
177D ILE* 1.3 64.8 + - - +
178D THR* 3.6 10.2 + - + +
190D ASP* 4.1 10.5 - - + -
191D VAL 3.2 7.0 - - - +
192D LEU* 4.3 7.0 - - + -
201D LEU* 4.8 4.3 - - + -
218D PHE* 3.7 31.9 - - + -
236D ILE* 3.8 39.9 - - + -
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PRO* 3.3 18.2 - - + +
141D ASN 4.6 0.2 - - - +
142D LEU* 4.3 6.5 - - + -
145D ALA* 3.6 35.9 - - + -
154D LEU* 4.3 4.3 - - + -
160D MET* 3.5 50.3 - - + +
163D ALA* 4.2 4.9 - - + -
164D ALA* 4.0 19.1 - - + +
167D ILE* 4.9 2.5 - - + -
175D VAL* 3.9 16.8 - - + -
176D VAL* 1.3 69.5 - - - +
178D THR* 1.3 63.3 + - - +
190D ASP* 3.2 7.1 - - - +
191D VAL* 2.9 34.2 + - + +
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Residues in contact with THR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D THR 4.5 7.2 + - - +
140D PRO 2.8 11.4 + - - +
141D ASN* 3.2 28.2 + - - +
142D LEU* 3.3 10.7 + - - +
160D MET* 4.3 2.0 - - - -
176D VAL* 4.0 21.8 - - + +
177D ILE* 1.3 74.9 - - - +
179D GLY* 1.3 59.7 + - - +
190D ASP* 3.1 11.0 - - - +
215D GLY* 6.2 1.1 - - - -
218D PHE* 4.0 22.0 - - + -
501D ADP 2.5 45.1 + - - +
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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
------------------------------------------------------------
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