Contacts of the strand formed by residues 16 - 25 (chain B) in PDB entry 5LXX
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 ARG 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B ASP* 1.3 84.2 + - - +
17B LEU* 1.3 64.6 + - - +
36B TYR* 3.4 22.8 + - - +
37B MET 3.3 5.8 - - - -
38B GLU* 2.8 29.3 + - + +
52B PRO* 3.5 32.4 - - - +
53B GLY 5.3 1.6 + - - -
55B VAL* 4.1 20.1 - - + +
56B LYS* 4.0 16.1 + - - +
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Residues in contact with LEU 17 (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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16B ARG* 1.3 75.9 - - - +
18B LEU* 1.3 64.6 + - - +
19B ILE* 4.8 2.5 - - + -
36B TYR* 3.5 2.8 - - - -
37B MET* 2.8 67.8 + - + +
55B VAL* 4.0 3.5 - - - +
56B LYS* 3.5 38.8 - - + +
58B ILE* 4.1 29.6 - - + -
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Residues in contact with LEU 18 (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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17B LEU* 1.3 76.2 - - - +
19B ILE* 1.3 67.7 + - - +
20B LYS* 3.5 31.2 - - + -
34B ASP* 4.4 4.9 - - + +
35B ILE 3.4 22.0 - - - +
36B TYR* 4.1 13.2 - - + -
49B LEU* 4.3 14.1 - - + +
51B VAL* 4.4 22.4 - - + -
55B VAL* 3.9 8.7 - - + -
56B LYS 2.9 8.3 + - - +
57B THR* 3.2 20.7 - - + +
58B ILE* 2.9 27.5 + - - +
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Residues in contact with ILE 19 (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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17B LEU* 4.8 2.0 - - + -
18B LEU* 1.3 75.2 - - - +
20B LYS* 1.3 63.0 + - - +
22B GLY* 5.1 1.6 - - - +
33B ALA 4.6 1.0 - - - +
34B ASP* 3.3 5.4 - - - +
35B ILE* 2.8 55.6 + - + +
37B MET* 3.7 26.0 - - + -
58B ILE* 3.5 31.2 - - + +
60B ALA* 3.9 24.7 - - + -
65B VAL* 4.6 21.3 - - + -
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Residues in contact with LYS 20 (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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18B LEU* 3.5 34.3 - - + -
19B ILE* 1.3 72.6 - - - +
21B GLY* 1.3 62.6 + - - +
22B GLY 3.4 1.3 - - - -
34B ASP* 3.4 20.2 - - - +
57B THR* 3.8 9.6 - - + -
58B ILE 2.9 9.3 + - - +
59B GLU* 3.6 31.9 + - - +
60B ALA* 2.8 30.3 + - - +
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Residues in contact with GLY 21 (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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19B ILE 4.1 0.4 + - - -
20B LYS* 1.3 73.8 - - - +
22B GLY* 1.3 57.0 + - - +
32B TYR* 4.8 2.9 - - - -
33B ALA 5.1 0.9 - - - -
34B ASP* 2.9 16.1 + - - -
59B GLU* 5.1 2.5 - - - -
60B ALA* 3.9 0.7 - - - -
61B HIS* 4.8 2.5 - - - -
62B SER* 2.7 38.9 + - - -
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Residues in contact with GLY 22 (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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19B ILE* 5.1 1.9 + - - +
20B LYS 3.4 4.2 + - - -
21B GLY* 1.3 80.1 - - - +
23B LYS* 1.3 61.9 + - - -
24B ILE* 3.8 1.1 - - - -
32B TYR* 3.5 8.3 - - - +
33B ALA 3.3 34.0 + - - +
35B ILE* 6.3 0.2 - - - -
60B ALA* 3.5 18.5 - - - +
63B ARG 3.6 5.8 - - - -
65B VAL* 3.9 8.7 - - - -
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Residues in contact with LYS 23 (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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480A LYS* 5.2 9.9 - - - +
21B GLY 4.2 0.2 + - - -
22B GLY* 1.3 70.2 - - - -
24B ILE* 1.3 70.4 + - - +
25B VAL* 3.4 25.1 + - - +
30B SER* 4.4 14.9 + - - -
31B PHE 3.7 9.2 - - - +
32B TYR* 3.6 42.8 - - + +
62B SER 3.9 11.8 - - - +
63B ARG 2.9 9.5 + - - +
64B MET* 3.4 22.6 - - - +
65B VAL* 2.8 25.5 + - - -
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Residues in contact with ILE 24 (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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22B GLY 3.8 1.1 - - - +
23B LYS* 1.3 71.7 - - - +
25B VAL* 1.3 61.5 + - - +
26B ASN* 3.9 28.4 + - - +
30B SER* 3.0 7.1 - - - -
31B PHE* 2.8 60.3 + - + +
33B ALA* 3.8 13.5 - - + +
35B ILE* 3.8 33.9 - - + -
45B ILE* 3.6 35.9 - - + -
65B VAL* 3.5 9.9 - - + +
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Residues in contact with VAL 25 (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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480A LYS* 5.7 0.7 - - - +
23B LYS* 3.5 36.8 - - - +
24B ILE* 1.3 75.6 - - - +
26B ASN* 1.3 68.0 + - - +
30B SER* 3.6 16.2 - - - +
64B MET* 4.1 22.7 - - + -
65B VAL 2.8 9.7 + - - +
66B ILE* 3.7 18.7 - - + +
67B PRO* 3.3 24.3 - - - +
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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