Contacts of the strand formed by residues 129 - 134 (chain B) in PDB entry 5MWF
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 LEU 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLU* 4.6 8.5 - - + +
32B LEU 3.4 14.6 - - - +
33B GLN* 3.5 21.1 - - - +
94B ALA 5.5 0.7 - - - +
95B THR* 4.5 1.2 - - - +
116B ARG* 3.7 36.6 - - - +
125B GLN* 3.9 27.5 + - - +
126B ASP* 3.6 22.9 + - + +
127B PRO 3.2 6.6 - - - +
128B GLY* 1.3 77.3 - - - +
130B VAL* 1.3 66.3 + - - +
131B VAL* 4.3 13.9 + - + -
178B TRP* 4.0 23.6 - - + -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE 3.7 1.0 - - - +
31B GLU* 3.4 5.9 - - - +
32B LEU* 2.9 47.1 + - + +
71B VAL* 5.2 0.9 - - + -
73B VAL* 3.9 33.2 - - + -
93B GLY* 4.0 23.8 - - - -
94B ALA* 4.3 8.1 - - - +
95B THR* 3.5 30.7 - - + -
128B GLY 4.8 0.7 - - - +
129B LEU* 1.3 72.9 - - - +
131B VAL* 1.3 65.8 + - - +
132B ILE* 4.2 13.2 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 4.1 33.0 - - + -
30B PHE 3.6 2.7 - - - +
31B GLU* 4.2 20.9 - - + +
92B HIS 5.1 2.3 - - - +
93B GLY* 5.4 1.4 - - - -
116B ARG* 5.7 2.2 - - - +
125B GLN* 4.9 9.3 - - - +
129B LEU* 4.3 16.6 - - + -
130B VAL* 1.3 81.4 - - - +
132B ILE* 1.3 68.2 + - - +
133B PRO* 3.6 11.7 - - + +
197B ARG* 5.3 4.7 - - - +
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Residues in contact with ILE 132 (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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29B TYR* 3.7 1.0 - - - -
30B PHE* 2.9 50.4 + - + +
73B VAL* 3.8 27.1 - - + -
75B LEU* 4.6 14.1 - - + -
90B TYR 4.2 4.7 - - - +
91B GLY* 3.7 30.3 - - - +
92B HIS* 3.8 33.9 - - - +
93B GLY 4.0 0.2 - - - +
130B VAL* 4.2 9.6 - - + -
131B VAL* 1.3 78.2 - - - +
133B PRO* 1.3 70.3 - - + +
134B PHE* 3.8 4.0 - - + -
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Residues in contact with PRO 133 (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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28B GLY 3.6 6.7 - - - +
29B TYR* 3.4 26.9 - - + -
90B TYR 4.7 2.6 - - - +
131B VAL* 3.6 14.6 - - + +
132B ILE* 1.3 96.8 - - + +
134B PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 134 (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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27B MET* 3.6 7.2 - - - +
28B GLY* 3.1 42.6 + - - +
29B TYR 3.5 26.9 - - - -
30B PHE* 3.8 3.6 - - + -
75B LEU* 5.9 1.8 - - + -
90B TYR 4.6 4.3 - - - +
132B ILE* 3.8 11.9 - - + +
133B PRO* 1.3 76.1 - - - +
135B GLN* 1.3 59.1 + - - +
136B PHE* 3.5 52.3 - + + -
138B TRP* 3.8 42.8 - + + -
196B VAL* 3.9 14.4 - - + -
207B CYS* 4.8 6.3 - - + -
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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