Contacts of the strand formed by residues 236 - 242 (chain B) in PDB entry 4MXW
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 THR 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.6 8.7 - - - +
94B GLY* 3.0 36.2 + - - -
102B LEU* 5.4 0.6 - - - +
104B TRP* 4.1 6.9 - - - -
138B LEU 3.1 6.3 - - - -
139B VAL* 3.5 11.0 - - + -
140B GLY 3.2 15.3 - - - +
223B ILE* 6.0 0.4 - - - -
229B VAL* 3.4 19.1 - - + +
230B ASP 3.3 24.1 + - - +
231B PHE* 4.3 5.4 - - - +
233B ARG 3.6 2.7 + - - -
235B LYS* 1.3 85.8 - - - +
237B PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 237 (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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91B HIS* 3.4 29.8 - + + +
92B LEU 3.1 15.5 - - - +
93B ILE* 4.4 2.9 - - + -
104B TRP* 3.8 9.4 - - - -
136B TYR* 3.6 17.3 - + - -
137B CYS* 3.4 1.3 - - - -
138B LEU* 2.9 66.1 + - + +
234B GLY* 4.3 14.1 - - - -
236B THR* 1.3 84.4 - - - +
238B PHE* 1.3 62.5 + - - +
179D LEU* 3.5 27.1 - - + -
207D PHE* 4.8 2.2 - - + -
208D GLY 3.1 31.6 - - - -
209D GLY* 4.1 4.9 - - - -
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Residues in contact with PHE 238 (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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92B LEU* 2.9 61.4 + - + +
104B TRP* 3.8 43.3 - + + -
119B PHE* 4.4 5.4 - + - -
125B LEU* 4.1 22.9 - - + -
135B LEU* 6.6 0.4 - - + -
136B TYR* 3.2 17.9 - - - +
137B CYS* 3.9 16.8 - - + -
161B SER* 5.7 2.0 - - - -
219B VAL* 4.2 24.9 - - + -
220B TYR* 5.0 2.9 - - - -
221B VAL* 3.7 23.8 - - + -
237B PHE* 1.3 76.7 - - - +
239B GLY* 1.3 65.2 + - - +
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Residues in contact with GLY 239 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B ALA* 3.2 15.9 - - - -
91B HIS* 4.2 0.2 - - - -
92B LEU* 4.8 2.0 - - - -
125B LEU* 5.4 0.4 - - - -
134B TYR 3.8 0.3 - - - +
135B LEU* 3.4 5.2 - - - +
136B TYR* 2.9 51.5 + - - +
238B PHE* 1.3 83.3 - - - +
240B ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 240 (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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89B ALA* 3.2 1.8 - - - -
90B ALA* 2.9 33.0 + - + +
125B LEU* 4.3 18.2 - - + -
127B LEU* 4.5 17.7 - - + -
133B TYR* 4.8 2.0 - - + -
134B TYR 3.2 6.3 - - - -
135B LEU* 3.4 24.7 - - + -
239B GLY* 1.3 73.7 - - - -
241B VAL* 1.3 69.7 + - - +
210D LEU* 4.0 1.7 - - - +
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Residues in contact with VAL 241 (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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87B LEU* 5.8 4.3 - - + -
88B PRO 3.8 9.6 - - - +
89B ALA* 4.4 4.7 - - + -
133B TYR* 3.1 7.1 - - - -
134B TYR* 2.9 37.1 + - + +
136B TYR* 5.3 1.1 - - + -
240B ALA* 1.3 72.6 - - - +
242B MET* 1.3 92.1 + - - +
243B VAL* 4.1 4.5 - - + +
132D LEU* 4.3 4.9 - - + -
210D LEU* 2.9 51.8 - - + -
243D VAL* 2.7 29.2 - - + -
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Residues in contact with MET 242 (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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62A LYS* 6.3 0.9 - - - +
87B LEU* 5.2 2.7 - - + +
88B PRO* 3.2 35.8 + - + +
129B GLN* 4.1 12.8 - - + +
130B ASP 3.6 20.4 - - - +
131B GLY* 4.0 7.9 - - - -
132B LEU 3.7 8.7 - - - +
133B TYR* 3.2 31.6 - - + -
241B VAL* 1.3 99.7 - - + +
243B VAL* 1.3 70.1 + - - +
243D VAL* 3.9 4.9 - - - +
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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