Contacts of the strand formed by residues 177 - 181 (chain D) in PDB entry 2I2X
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 MET 177 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D VAL* 3.2 16.7 - - + +
127D VAL 3.1 21.8 + - - -
147D LEU* 6.0 0.7 - - - -
175D PRO* 3.2 5.9 - - - +
176D ILE* 1.3 90.5 - - + +
178D LEU* 1.3 73.7 + - - +
179D THR* 4.5 8.1 - - + -
205D ILE* 4.3 6.7 - - - -
206D PRO* 3.6 24.2 - - + +
208D ALA* 4.1 10.5 - - + -
234D ALA 4.2 2.5 - - - +
237D ILE* 3.5 57.7 - - + +
238D ALA* 3.8 12.1 - - - -
241D ILE* 3.6 15.3 - - + -
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D VAL* 3.3 39.5 - - + +
129D HIS* 3.9 11.0 - - + +
166D VAL* 3.9 20.4 - - + -
170D VAL* 4.5 6.3 - - + -
175D PRO* 5.5 0.4 - - + -
177D MET* 1.3 77.8 - - - +
179D THR* 1.3 61.8 - - - +
194D VAL* 3.8 22.2 - - + -
198D LEU* 3.8 27.6 - - + -
205D ILE* 4.1 13.8 - - + +
206D PRO 3.2 8.3 + - - +
207D PHE* 3.3 22.5 - - + -
208D ALA 3.0 23.0 + - - -
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Residues in contact with THR 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D VAL* 4.1 16.8 - - + -
127D VAL 2.8 8.3 + - - +
128D CYS* 3.1 28.2 - - - +
129D HIS* 2.8 35.3 + - - -
140D LYS* 5.7 0.7 - - - +
143D VAL* 4.2 17.7 - - + +
147D LEU* 4.6 2.2 - - + -
177D MET* 4.5 6.3 - - + -
178D LEU* 1.3 77.3 - - - +
180D GLY* 1.3 54.3 + - - +
181D THR* 6.0 0.2 - - - -
207D PHE* 3.7 4.9 - - - -
208D ALA* 3.3 12.1 - - + -
234D ALA* 4.9 3.1 - - + -
500D B13 3.5 23.1 - - - +
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D HIS* 3.4 21.8 - - - -
179D THR* 1.3 74.0 - - - +
181D THR* 1.3 65.0 + - - -
191D PHE* 3.3 11.9 - - - -
207D PHE* 3.5 10.0 - - - -
208D ALA 3.0 7.6 + - - +
210D GLY 3.2 22.3 + - - -
500D B13 3.3 5.9 - - - -
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Residues in contact with THR 181 (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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129D HIS 3.3 12.1 + - - -
130D VAL* 3.6 15.3 - - + +
131D ALA 3.0 22.7 + - - -
134D ASP* 6.4 0.2 - - - -
136D HIS 4.4 11.4 - - - +
140D LYS* 4.1 17.2 - - - +
180D GLY* 1.3 72.2 + - - -
182D ALA* 1.3 62.9 + - - +
183D LEU* 3.6 25.8 - - + -
191D PHE* 3.3 4.6 - - - -
210D GLY 3.3 4.9 - - - -
211D GLY* 4.2 1.1 - - - -
500D B13 2.5 40.0 + - + +
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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