Contacts of the strand formed by residues 136 - 142 (chain B) in PDB entry 4MZF
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 ALA 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B GLY 4.0 1.8 + - - -
135B LYS* 1.3 74.4 - - - +
137B VAL* 1.3 63.7 + - - +
152B ARG* 5.5 8.1 - - + -
153B GLY 3.4 11.4 - - - +
154B MET* 4.4 4.4 - - + +
192B ILE* 3.9 0.5 - - - -
193B MET* 2.8 45.9 + - + +
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Residues in contact with VAL 137 (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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135B LYS* 3.7 11.2 - - + +
136B ALA* 1.3 81.1 - - - +
138B GLU* 1.3 65.6 + - - +
139B HIS* 4.7 1.8 - - + -
152B ARG* 3.4 8.3 - - - +
153B GLY* 2.9 48.0 + - - +
154B MET 4.2 0.9 - - - +
155B VAL* 3.8 15.0 - - + -
168B ILE* 3.9 17.9 - - + -
190B LEU* 3.8 20.9 - - + -
191B ARG 3.1 7.9 - - - +
192B ILE* 3.6 28.5 - - + -
193B MET* 4.2 3.6 - - - +
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Residues in contact with GLU 138 (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 VAL* 1.3 74.4 - - - +
139B HIS* 1.3 60.9 + - - +
140B MET 3.8 1.0 + - - -
150B GLU* 3.4 40.1 - - - +
151B TRP 3.7 0.4 - - - -
152B ARG* 3.3 49.6 + - - -
189B ASP 3.8 1.6 - - - +
190B LEU* 3.4 4.5 - - - -
191B ARG* 2.8 52.7 + - - +
193B MET* 3.4 28.0 - - + +
303B MG 4.0 9.8 - - - -
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Residues in contact with HIS 139 (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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2A ARG* 4.3 1.6 + - - -
137B VAL* 4.7 4.0 - - + -
138B GLU* 1.3 70.9 - - - +
140B MET* 1.3 72.6 + - - +
141B PHE* 3.4 28.6 - + - -
150B GLU* 4.5 0.9 - - - -
151B TRP* 2.8 39.3 + - - +
168B ILE* 3.9 5.1 - - - +
170B TYR* 2.7 38.4 + - + -
179B TYR* 3.9 7.9 - + - -
181B LEU* 3.5 21.7 - - + +
184B ASP* 2.7 28.6 + - - -
189B ASP 3.6 10.1 - - - -
190B LEU* 3.8 17.3 - - + -
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Residues in contact with MET 140 (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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1A ALA* 3.7 14.8 - - + +
2A ARG* 4.4 3.6 + - - +
138B GLU 3.8 1.8 + - - +
139B HIS* 1.3 80.4 + - - +
141B PHE* 1.3 69.3 + - - +
142B GLU* 6.1 0.2 - - + -
148B LYS* 3.5 49.8 - - + +
149B ASP 3.7 18.6 - - - -
150B GLU* 3.3 35.0 - - + +
184B ASP* 5.0 0.5 - - - +
188B GLY 5.4 0.7 - - - +
189B ASP* 2.8 42.2 + - - +
191B ARG* 5.6 1.6 - - - +
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Residues in contact with PHE 141 (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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1A ALA* 4.1 3.4 - - - -
2A ARG* 3.2 37.2 - - + +
3A THR 4.6 3.4 - - - -
4A M3L 3.5 47.6 - - + +
139B HIS* 3.4 53.2 - + + -
140B MET* 1.3 81.1 - - - +
142B GLU* 1.3 64.8 + - - +
148B LYS* 3.8 0.5 - - - -
149B ASP* 2.7 39.2 + - + +
151B TRP* 3.9 15.5 - + + +
170B TYR* 3.8 2.7 - + - -
179B TYR* 3.7 27.1 - + - -
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Residues in contact with GLU 142 (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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1A ALA* 2.8 46.0 + - + +
2A ARG 2.8 8.8 + - - +
3A THR* 3.5 28.6 - - - +
4A M3L 4.3 2.8 + - - +
141B PHE* 1.3 77.3 - - - +
143B THR* 1.3 67.1 + - - +
146B GLY* 4.3 18.3 - - - +
147B SER 3.5 14.4 - - - +
148B LYS* 4.9 1.1 - - - -
149B ASP* 4.4 1.1 - - - +
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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