Contacts of the strand formed by residues 168 - 172 (chain B) in PDB entry 5M7T
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 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B GLU* 2.7 25.7 + - - +
133B PHE 3.5 13.4 + - - -
134B ILE* 3.8 12.3 - - - -
135B TYR 3.1 9.9 + - - -
166B CYS* 3.1 22.6 - - - -
167B ARG* 1.3 90.3 + - - +
169B PHE* 1.3 63.1 + - - +
211B THR* 3.4 23.9 + - - -
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Residues in contact with PHE 169 (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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134B ILE* 3.4 8.4 - - - +
135B TYR* 3.1 14.4 - - + -
158B LEU* 3.6 27.4 - - + -
161B VAL* 3.4 27.6 - - + -
162B SER* 3.9 17.0 - - - -
166B CYS* 3.4 36.3 - - - -
167B ARG* 3.6 16.2 - - - -
168B SER* 1.3 75.9 - - - +
170B ALA* 1.3 63.8 + - - +
171B LEU* 5.8 0.4 - - + -
206B LEU* 3.9 24.0 - - + -
209B PRO* 4.5 8.5 - - + -
211B THR 3.3 7.1 + - - -
212B PHE* 3.3 25.1 - - + -
213B LEU 3.0 20.4 + - - -
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Residues in contact with ALA 170 (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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94B LEU* 4.3 5.2 - - + -
134B ILE* 4.2 6.7 - - + -
135B TYR 2.8 6.7 + - - +
136B ALA* 3.2 20.7 - - + -
137B ILE* 3.0 24.9 + - - +
158B LEU* 5.4 0.3 - - - +
169B PHE* 1.3 79.5 - - - +
171B LEU* 1.3 71.4 + - - +
172B LEU* 4.3 7.6 - - + -
212B PHE* 4.7 1.5 - - - -
213B LEU* 3.1 27.1 - - + +
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Residues in contact with LEU 171 (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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137B ILE* 3.5 23.3 - - + +
139B PRO* 5.0 3.8 - - + -
154B LEU* 4.4 12.8 - - + -
158B LEU* 4.2 15.3 - - + -
169B PHE* 5.8 0.2 - - + -
170B ALA* 1.3 82.1 - - - +
172B LEU* 1.3 62.1 + - - +
173B PHE* 3.9 22.4 - - + -
198B ILE* 4.6 2.0 - - + +
199B THR* 3.9 37.9 - - + +
202B ILE* 4.3 17.5 - - + -
212B PHE* 4.1 14.9 - - + -
213B LEU 3.0 8.3 + - - +
214B PHE* 3.4 7.2 - - + -
215B CYS 3.0 23.0 + - - +
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Residues in contact with LEU 172 (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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94B LEU* 5.5 1.3 - - + -
96B ALA* 3.9 28.0 - - + +
98B LYS* 5.2 2.5 - - - +
103B HIS* 3.9 7.2 - - + +
136B ALA* 3.9 13.5 - - + -
137B ILE 3.0 10.0 + - - +
138B SER* 3.5 40.5 - - - +
139B PRO* 4.0 2.0 - - - +
140B GLY* 4.5 2.1 + - - -
170B ALA* 4.3 6.3 - - + -
171B LEU* 1.3 76.8 - - - +
173B PHE* 1.3 69.5 + - - +
174B ASP* 3.4 20.3 - - - +
215B CYS* 3.7 21.8 - - + +
248B LEU* 4.1 15.9 - - + -
278B TRP* 4.3 14.1 - - + -
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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
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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