Contacts of the strand formed by residues 38 - 44 (chain B) in PDB entry 2LAG
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 HIS 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B PRO 3.5 0.8 - - - -
37B THR* 1.3 97.7 - - + +
39B TYR* 1.3 69.3 + - - +
60B ASN* 4.3 26.4 - - - +
61B THR 3.2 11.7 - - - +
62B THR* 5.6 1.1 - - + -
86B PHE* 3.0 61.8 + + + +
88B GLY* 3.0 43.7 + - - -
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Residues in contact with TYR 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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27B TRP* 3.4 40.8 - + + +
29B LEU* 3.9 35.6 - - + +
31B ASN* 5.2 1.4 + - - -
36B PRO* 2.8 42.6 + - + +
37B THR* 4.6 4.4 - - - -
38B HIS* 1.3 82.4 - - - +
40B THR* 1.3 63.8 + - - +
58B CYS 3.8 3.9 - - - +
59B ALA 3.8 1.0 - - - -
60B ASN* 3.0 16.6 + - - -
61B THR* 3.0 20.9 + - - +
62B THR 5.0 5.4 - - - -
63B ARG 3.9 12.6 - - - -
64B SER* 4.7 9.6 - - - -
83B LEU* 4.4 7.6 - - + -
84B GLU 4.0 6.3 - - - +
85B GLY* 4.6 11.2 - - - -
86B PHE* 5.2 0.4 - - - -
93B PHE* 6.2 0.9 - + - -
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Residues in contact with THR 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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27B TRP* 5.8 0.4 - - - -
39B TYR* 1.3 76.5 - - - +
41B LEU* 1.3 62.4 + - - +
42B LEU* 3.7 20.6 + - + +
54B VAL* 4.1 10.5 - - + -
58B CYS 3.7 2.5 - - - -
59B ALA* 3.9 16.6 - - + -
60B ASN* 3.0 22.7 + - - +
83B LEU* 4.1 5.0 - - - +
84B GLU* 3.2 32.9 + - - +
86B PHE* 3.5 30.4 - - + -
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Residues in contact with LEU 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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14B PHE* 4.8 1.3 - - + -
25B LEU* 3.8 22.4 - - + -
27B TRP* 3.6 39.9 - - + -
40B THR* 1.3 73.8 - - - +
42B LEU* 1.3 75.8 + - - +
43B TYR* 4.8 4.0 - - + -
54B VAL* 3.7 6.8 - - - +
55B VAL* 3.2 36.4 + - + +
58B CYS* 3.1 22.4 + - + +
66B CYS* 5.0 0.4 - - + -
72B TRP* 6.2 0.9 - - + -
81B THR* 4.1 16.2 - - + -
82B VAL 3.4 17.7 - - - +
83B LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 42 (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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40B THR* 3.7 22.4 - - + +
41B LEU* 1.3 87.4 - - - +
43B TYR* 1.3 64.7 + - - +
52B LEU* 4.0 39.0 - - + +
53B LYS 3.4 6.1 - - - +
54B VAL* 3.9 19.3 - - + -
81B THR* 4.1 0.2 - - - -
82B VAL* 3.3 43.7 + - + +
84B GLU* 3.9 26.0 - - + +
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Residues in contact with TYR 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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27A PHE* 4.3 4.2 - - - -
41B LEU* 4.8 5.6 - - + -
42B LEU* 1.3 75.8 - - - +
44B THR* 1.3 63.1 + - - +
52B LEU 3.9 0.3 - - - -
53B LYS* 2.8 79.9 + - + +
54B VAL 4.5 3.6 - - - -
55B VAL* 3.4 29.2 - - + -
68B LEU* 5.1 0.7 - - + -
71B GLU* 3.3 37.3 + - + +
72B TRP* 3.5 28.3 - + + +
79B TYR* 3.4 36.3 - + + -
80B VAL 3.4 13.7 - - - +
81B THR* 5.2 1.1 - - + -
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Residues in contact with THR 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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27A PHE* 3.4 30.3 - - + -
43B TYR* 1.3 84.3 - - - +
45B ILE* 1.3 80.1 + - - +
48B LYS 4.2 3.5 + - - -
49B PRO* 4.5 11.2 - - + -
50B GLU 5.0 0.2 - - - +
51B ASP* 2.7 34.4 + - - +
52B LEU* 4.5 0.4 - - - -
53B LYS* 5.5 1.1 - - - -
79B TYR* 3.3 12.9 - - - -
80B VAL* 2.8 32.3 + - + -
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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