Contacts of the strand formed by residues 35 - 41 (chain B) in PDB entry 3LQM
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 LYS 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ASN 3.4 4.9 - - - +
31B SER* 3.4 3.2 - - - -
32B VAL* 2.9 31.7 + - + +
33B ASN* 3.2 3.2 + - + +
34B PHE* 1.3 75.8 - - - +
36B ASN* 1.3 58.7 + - - +
37B ILE* 3.6 22.3 + - + +
75B ASP* 4.3 12.9 + - - -
77B SER* 3.4 10.5 - - - +
137B GLU* 3.9 35.5 + - + +
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Residues in contact with ASN 36 (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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29B MET* 3.5 22.2 - - + -
30B ASN 4.0 0.9 - - - -
31B SER* 2.7 24.7 + - - -
34B PHE* 3.2 23.3 + - - +
35B LYS* 1.3 68.3 - - - +
37B ILE* 1.3 64.4 + - - +
75B ASP 3.7 0.3 - - - -
76B PHE* 2.8 54.8 + - - +
77B SER* 3.1 14.6 + - - +
79B LEU* 4.3 10.5 + - - +
105B PHE* 3.6 20.9 - - + -
107B PRO* 4.4 7.5 - - - +
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Residues in contact with ILE 37 (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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29B MET* 3.5 3.3 - - - -
30B ASN* 2.9 45.8 + - + +
35B LYS* 4.3 31.6 - - + +
36B ASN* 1.3 73.9 - - - +
38B LEU* 1.3 71.6 + - - +
39B GLN* 3.4 18.2 + - + +
73B GLU* 3.8 26.9 - - + +
74B CYS 3.6 4.7 - - - +
75B ASP* 3.7 36.8 - - + +
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Residues in contact with LEU 38 (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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27B VAL* 3.9 11.4 - - + -
28B ARG 3.6 17.5 - - - +
29B MET* 3.8 7.6 - - + +
36B ASN 3.8 2.0 + - - -
37B ILE* 1.3 70.5 - - - +
39B GLN* 1.3 58.6 + - - +
40B TRP* 3.6 22.7 - - + -
54B ALA* 4.3 9.4 - - + -
73B GLU* 3.1 7.3 - - - +
74B CYS 2.9 32.4 + - - +
76B PHE* 3.7 36.1 - - + -
87B LEU* 4.4 16.8 - - + -
88B ARG* 4.9 2.7 - - - +
89B VAL* 4.3 14.6 - - + -
103B ILE* 3.8 27.1 - - + -
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Residues in contact with GLN 39 (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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26B ASN 3.7 0.3 - - - +
27B VAL* 3.4 1.9 - - - +
28B ARG* 2.8 64.3 + - - +
30B ASN* 3.3 34.3 + - + +
37B ILE* 3.6 19.8 - - + +
38B LEU* 1.3 79.0 - - - +
40B TRP* 1.3 68.9 + - - +
72B THR 3.6 7.4 - - - +
73B GLU* 3.5 23.3 + - + -
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Residues in contact with TRP 40 (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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24B PRO* 3.8 18.6 - - + -
25B GLU 3.5 9.9 - - - +
26B ASN 3.7 0.2 - - - -
27B VAL* 3.9 16.4 - - + -
28B ARG* 3.5 10.5 + - - +
38B LEU* 3.6 38.1 - - + -
39B GLN* 1.3 85.6 - - - +
41B GLU* 1.3 74.7 + - - +
52B PHE* 3.5 41.0 - + + -
54B ALA* 4.7 3.6 - - + -
69B THR* 4.5 4.9 - - + -
71B LEU 3.4 19.1 - - - -
72B THR* 3.2 36.6 + - + +
73B GLU* 3.5 22.7 - - - -
74B CYS* 3.8 9.6 - - + -
89B VAL* 4.2 18.8 - - + -
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Residues in contact with GLU 41 (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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24B PRO* 3.9 3.5 - - - +
25B GLU* 2.8 44.4 + - + +
26B ASN* 2.9 31.6 + - - +
28B ARG* 3.9 13.6 + - - +
40B TRP* 1.3 83.5 - - - +
42B SER* 1.3 66.0 + - - +
43B PRO* 3.6 2.1 - - - +
72B THR* 4.8 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