Contacts of the strand formed by residues 129 - 134 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 4.6 12.1 - - + +
32A LEU 3.5 12.8 - - - +
33A GLN* 3.6 20.4 + - - +
94A ALA 5.6 0.7 - - - +
95A THR* 4.5 0.9 - - - +
116A ARG* 3.7 34.5 - - - +
125A GLN* 6.0 0.2 - - + -
126A ASP* 3.8 18.4 + - + +
127A PRO 3.2 8.7 - - - +
128A GLY* 1.3 78.2 - - - +
130A VAL* 1.3 68.5 + - - +
131A VAL* 4.1 19.1 + - + +
178A TRP* 4.1 24.5 - - + -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.6 1.7 - - + +
31A GLU* 3.3 6.6 - - - +
32A LEU* 2.9 46.2 + - + +
71A VAL* 5.3 0.9 - - + -
73A VAL* 4.0 28.7 - - + -
93A GLY* 4.0 27.4 - - - -
94A ALA 4.3 8.5 - - - +
95A THR* 3.5 26.2 - - + -
128A GLY 4.8 1.3 - - - +
129A LEU* 1.3 78.3 - - - +
131A VAL* 1.3 65.1 + - - +
132A ILE* 4.2 13.7 - - + -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 4.1 32.8 - - + -
30A PHE 3.4 2.7 - - - +
31A GLU* 4.2 16.2 - - + +
92A HIS 5.2 1.7 - - - +
129A LEU* 4.1 23.3 + - + +
130A VAL* 1.3 80.0 - - - +
132A ILE* 1.3 67.1 + - - +
133A PRO* 3.6 11.6 - - + +
197A ARG* 5.5 2.5 - - - +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.7 1.1 - - - -
30A PHE* 2.8 50.4 + - + +
73A VAL* 4.0 26.0 - - + -
75A LEU* 4.5 15.3 - - + -
90A TYR 4.0 7.0 - - - +
91A GLY* 3.6 30.5 - - - +
92A HIS* 3.8 34.1 - - - +
93A GLY 4.0 0.9 - - - +
130A VAL* 4.2 9.6 - - + -
131A VAL* 1.3 77.2 - - - +
133A PRO* 1.3 69.4 - - + +
134A PHE* 3.9 3.4 + - + -
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Residues in contact with PRO 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 6.5 1.3 - - + -
28A GLY 3.5 7.6 - - - +
29A TYR* 3.5 27.8 - - + -
90A TYR 4.6 2.6 - - - +
131A VAL* 3.6 15.5 - - + +
132A ILE* 1.3 96.6 - - + +
134A PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.4 9.6 - - - +
28A GLY* 3.0 55.5 + - - +
29A TYR 3.4 26.9 - - - -
30A PHE* 3.9 2.9 - - + -
75A LEU* 5.9 1.6 - - + -
90A TYR 4.7 4.0 - - - +
132A ILE* 3.9 11.4 - - + -
133A PRO* 1.3 75.6 - - - +
135A GLN* 1.3 59.4 + - - +
136A PHE* 3.5 53.4 - + + -
138A TRP* 3.8 41.7 - + + -
196A VAL* 3.9 15.3 - - + -
207A CYS* 4.6 7.6 - - + -
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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