Contacts of the strand formed by residues 132 - 140 (chain B) in PDB entry 5LEZ
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 VAL 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 3.4 7.1 - - - +
76B VAL* 4.1 4.7 - - + -
77B ALA 3.6 7.4 - - - +
78B GLY 5.3 0.2 - - - +
79B ILE 3.6 5.8 - - - +
82B ASP* 3.5 30.1 - - + +
83B ALA* 3.5 29.8 - - + +
86B LEU* 4.0 15.9 - - + -
118B LYS* 4.1 6.6 + - - +
130B PHE 3.2 3.9 + - - +
131B GLY* 1.3 84.1 - - - +
133B SER* 1.3 71.8 + - - +
134B LEU* 3.8 18.4 - - + -
151B ASP 3.8 2.8 - - - -
152B PRO* 3.4 23.0 - - - +
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Residues in contact with SER 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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25B MET* 5.8 0.3 - - - +
28B ILE* 3.5 30.4 - - - +
76B VAL* 3.5 3.3 - - - -
77B ALA 2.9 31.4 + - - -
132B VAL* 1.3 74.1 - - - +
134B LEU* 1.3 62.3 + - - +
149B GLN* 5.8 0.2 + - - -
150B SER 3.2 7.9 - - - -
151B ASP* 3.2 26.7 - - - +
164B ILE* 3.5 23.7 - - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B CYS* 4.1 10.1 - - - -
75B SER 3.3 4.0 - - - +
76B VAL* 3.7 24.0 - - + -
86B LEU* 4.3 13.9 - - + -
87B THR* 4.5 4.7 - - + -
90B LEU* 4.0 26.2 - - + -
114B LEU* 4.4 3.1 - - + -
118B LYS* 3.6 26.0 - - - +
132B VAL* 3.8 14.4 - - + -
133B SER* 1.3 81.0 - - - +
135B LEU* 1.3 66.2 + - - +
136B TYR* 3.7 22.0 - - + +
149B GLN* 3.3 6.2 - - - +
150B SER* 2.8 34.2 + - - +
164B ILE* 4.2 1.1 - - - -
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Residues in contact with LEU 135 (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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34B CYS* 3.6 25.1 - - - +
35B LEU* 3.5 9.6 - - - +
36B GLY* 3.5 30.5 - - - +
45B LEU* 3.7 15.8 - - + +
74B CYS* 3.0 5.5 - - - +
75B SER* 2.8 37.8 + - - +
134B LEU* 1.3 79.7 - - - +
136B TYR* 1.3 61.6 + - - +
147B LEU* 4.6 3.4 - - + -
148B TYR 3.3 3.8 - - - +
149B GLN* 3.8 19.5 - - + +
162B THR* 3.8 26.7 - - + +
164B ILE* 3.8 16.8 - - + -
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Residues in contact with TYR 136 (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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68B LEU* 4.2 10.3 - - + -
72B MET* 4.5 12.3 - - + -
73B ALA 3.5 6.7 - - - +
74B CYS* 4.2 11.4 - - + -
90B LEU* 3.9 29.4 - - + -
110B LEU* 5.6 0.7 - - + -
111B VAL* 3.6 36.9 + - + +
114B LEU* 3.4 22.7 - - - +
134B LEU* 3.7 20.5 - - + +
135B LEU* 1.3 75.1 - - - +
137B ILE* 1.3 62.8 + - - +
146B GLN 3.8 0.7 - - - +
147B LEU* 3.2 6.1 - - - +
148B TYR* 2.8 52.2 + - + +
150B SER* 2.7 38.0 + - - -
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Residues in contact with ILE 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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43B VAL* 3.3 41.1 - - + +
44B LEU* 3.9 4.7 - - - +
45B LEU* 3.8 35.9 - - + +
72B MET* 3.3 7.6 - - - +
73B ALA* 2.8 50.9 + - + +
107B CYS* 6.0 0.2 - - - -
135B LEU 4.2 0.6 + - - -
136B TYR* 1.3 78.2 - - - +
138B GLY* 1.3 59.2 + - - +
146B GLN 3.4 3.8 - - - -
147B LEU* 3.8 13.9 - - + -
214B ALA* 4.6 5.8 - - + +
215B THR 4.8 1.1 - - - -
216B LEU* 3.6 28.9 - - + +
225B ILE* 6.1 1.1 - - + -
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Residues in contact with GLY 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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43B VAL* 4.2 1.6 - - - +
71B ASP 3.2 13.0 - - - -
72B MET* 4.1 0.4 - - - -
107B CYS* 3.9 17.2 - - - +
137B ILE* 1.3 76.3 - - - +
139B TRP* 1.3 60.6 + - - -
144B GLY 3.7 0.2 - - - +
145B PHE* 3.4 4.3 - - - -
146B GLN 2.9 33.7 + - - +
216B LEU* 3.6 14.3 - - - +
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Residues in contact with TRP 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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71B ASP* 3.0 36.9 + - - +
104B PRO* 6.4 1.6 - - + -
105B ILE 5.5 0.9 - - - +
107B CYS* 3.8 6.3 - - - -
138B GLY* 1.3 75.0 - - - +
140B ASP* 1.3 70.9 + - - +
141B LYS* 3.7 28.7 - - + -
144B GLY* 3.5 29.4 - - - -
145B PHE* 3.7 15.0 - + + -
216B LEU* 3.9 10.7 - - + +
218B ARG* 3.3 63.4 - - + +
223B THR* 4.0 13.7 - - - +
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Residues in contact with ASP 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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71B ASP* 5.6 0.7 - - - -
104B PRO* 6.1 2.2 - - + +
105B ILE 4.8 2.2 - - - +
106B PRO* 3.5 26.6 - - + +
107B CYS* 3.0 24.9 + - - +
108B GLU* 4.6 0.3 + - - +
139B TRP* 1.3 89.0 - - - +
141B LYS* 1.3 58.1 + - + +
142B HIS* 2.8 20.5 + - - +
143B TYR* 2.9 15.4 + - - -
144B GLY* 2.8 34.2 + - - -
146B GLN* 3.1 19.7 + - - +
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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