Contacts of the strand formed by residues 125 - 129 (chain W) 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 SER 125 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122W LYS* 5.7 3.1 + - - -
123W GLY 4.3 0.4 + - - -
124W PRO* 1.3 74.1 + - - +
126W VAL* 1.3 62.9 + - - +
127W PHE* 3.5 30.5 - - - -
140W LEU 3.3 3.8 - - - +
141W VAL* 3.4 2.9 - - - -
142W LYS* 2.9 36.7 + - - +
143W ASP* 5.9 1.9 - - - +
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Residues in contact with VAL 126 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123V GLU* 5.7 0.3 - - - +
124W PRO* 4.8 5.8 - - + +
125W SER* 1.3 78.6 - - - +
127W PHE* 1.3 69.6 + - - +
139W CYS* 3.7 17.7 - - - -
140W LEU 3.4 4.0 - - - +
141W VAL* 4.2 10.8 - - + -
197W VAL* 3.9 21.3 - - + -
206W VAL* 3.6 27.1 - - + -
208W LYS* 3.5 49.2 - - + +
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Residues in contact with PHE 127 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121V SER* 3.1 20.4 - - - +
123V GLU* 4.2 15.0 - - + -
124V GLN* 3.6 47.6 - - + -
127V SER* 5.4 8.3 - - - -
125W SER* 3.5 32.8 - - - -
126W VAL* 1.3 84.3 - - - +
128W PRO* 1.3 65.2 - - - +
129W LEU* 5.9 0.4 - - + -
139W CYS* 3.7 1.4 - - - -
140W LEU* 2.8 57.7 + - + +
142W LYS* 4.4 17.3 - - + -
143W ASP* 6.0 0.2 - - - -
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Residues in contact with PRO 128 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V PRO 5.3 0.9 - - - +
121V SER* 3.5 24.6 + - - -
123V GLU* 3.8 27.1 - - - +
127W PHE* 1.3 88.1 - - + +
129W LEU* 1.3 67.8 + - - +
130W ALA* 3.8 6.8 + - + +
138W GLY 3.8 0.7 - - - +
139W CYS* 4.8 0.4 - - - -
208W LYS* 4.2 16.8 - - + +
209W LYS 4.4 5.2 - - - +
210W VAL* 3.5 34.5 - - + -
211W GLU 5.2 2.2 - - - +
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Residues in contact with LEU 129 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118V PHE* 3.4 34.2 - - + -
119V PRO 5.0 7.0 - - - +
120V PRO* 5.9 0.4 - - + -
121V SER* 5.6 3.4 - - - +
131V SER 5.8 3.4 - - - +
133V VAL* 3.5 27.8 - - + +
127W PHE* 5.9 0.4 - - + -
128W PRO* 1.3 80.8 - - - +
130W ALA* 1.3 64.2 + - - +
137W LEU* 3.4 5.5 - - - +
138W GLY* 2.9 42.5 + - - +
139W CYS 4.2 11.2 - - - +
140W LEU* 4.2 24.0 - - + +
178W SER* 4.3 19.1 - - - -
180W VAL* 4.6 8.5 - - + -
210W VAL* 3.6 2.4 - - - +
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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