Contacts of the strand formed by residues 42 - 48 (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 GLY 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LEU* 4.0 0.3 - - - +
39B ALA* 2.8 34.9 + - - +
40B ASN 3.6 0.4 - - - -
41B ASP* 1.3 81.5 + - - +
43B VAL* 1.3 68.4 + - - +
145B PHE* 3.8 12.2 - - - -
186B LEU* 4.2 13.2 - - - -
216B LEU 3.4 13.0 - - - -
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Residues in contact with VAL 43 (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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37B ILE 3.5 18.8 - - - +
38B LEU* 4.1 7.4 - - + -
42B GLY* 1.3 79.3 - - - +
44B LEU* 1.3 64.7 + - - +
137B ILE* 3.3 36.0 - - + +
138B GLY 4.2 3.8 - - - +
145B PHE* 3.8 28.3 - - + -
146B GLN 3.9 17.9 - - - +
147B LEU* 4.4 7.0 - - + -
186B LEU* 4.0 5.8 - - - +
215B THR* 3.5 2.4 - - - -
216B LEU* 2.8 38.1 + - + +
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Residues in contact with LEU 44 (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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35B LEU* 4.0 9.9 - - + -
36B GLY* 3.2 5.4 - - - -
37B ILE* 3.1 38.6 + - + +
43B VAL* 1.3 74.9 - - - +
45B LEU* 1.3 80.0 + - - +
46B ALA* 4.0 4.0 - - + +
137B ILE* 3.9 7.2 - - - +
186B LEU* 4.5 9.4 - - + -
189B ALA* 3.5 46.9 - - + +
190B LEU* 3.6 25.1 - - + +
193B ALA* 3.9 21.5 - - + -
213B ILE* 4.8 0.9 - - + -
214B ALA 3.2 10.8 - - - +
215B THR* 4.5 1.1 - - + -
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Residues in contact with LEU 45 (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* 5.9 0.2 - - - -
35B LEU 3.3 10.3 - - - +
36B GLY* 4.3 1.8 - - - -
44B LEU* 1.3 78.1 - - - +
46B ALA* 1.3 60.8 + - - +
65B ILE* 3.7 29.8 - - + -
73B ALA* 4.5 0.7 - - + -
74B CYS* 3.7 31.2 - - - +
75B SER* 3.9 7.9 - - - +
135B LEU* 3.7 32.1 - - + +
137B ILE* 3.8 39.7 - - + -
212B GLU 3.9 0.8 - - - +
213B ILE* 3.3 7.1 - - - +
214B ALA* 2.9 33.3 + - + +
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Residues in contact with ALA 46 (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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33B THR 4.2 0.2 - - - +
34B CYS* 3.6 2.1 - - - -
35B LEU* 2.8 60.9 + - + +
44B LEU* 4.0 1.8 - - + +
45B LEU* 1.3 75.0 - - - +
47B ALA* 1.3 61.5 + - - +
193B ALA* 4.1 14.4 - - + -
197B LEU* 4.1 15.6 - - + +
212B GLU 3.3 5.4 - - - -
213B ILE* 3.9 16.8 - - + -
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Residues in contact with ALA 47 (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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33B THR 3.3 9.4 - - - +
34B CYS* 4.2 6.1 - - - -
46B ALA* 1.3 75.3 - - - +
48B GLU* 1.3 68.4 + - - +
49B ARG 3.7 0.2 + - - -
64B LYS* 4.2 14.4 - - + -
65B ILE* 4.9 4.7 - - + -
75B SER* 4.1 19.7 - - - +
197B LEU* 4.6 4.1 - - - +
211B VAL* 3.4 5.6 - - - +
212B GLU* 2.8 42.0 + - + +
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Residues in contact with GLU 48 (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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32B GLY* 4.2 1.7 - - - -
33B THR* 2.8 51.0 + - + +
47B ALA* 1.3 71.7 - - - +
49B ARG* 1.3 68.3 + - - +
50B ARG* 3.2 39.5 + - - -
64B LYS* 3.3 28.2 + - - +
166B ASN* 4.7 1.4 + - - +
197B LEU* 5.0 3.4 - - + +
201B MET* 3.8 35.3 - - + +
210B LYS 3.8 3.8 - - - -
211B VAL* 4.8 4.0 - - - +
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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