Contacts of the strand formed by residues 18 - 25 (chain B) in PDB entry 1LVB
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 ILE 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE 3.8 7.2 - - - +
15B SER* 3.2 23.1 + - - +
16B SER 4.5 2.4 - - - +
17B THR* 1.3 81.6 - - - +
19B CYS* 1.3 63.2 + - - +
33B TYR* 3.6 32.5 - - + -
34B GLY 3.3 11.4 - - - +
35B ILE* 5.0 0.9 - - + -
59B SER* 4.1 6.1 - - - -
60B LEU* 5.0 1.4 + - - +
112B VAL* 3.5 26.2 - - + +
113B THR* 4.0 7.2 - - - -
114B THR* 3.5 26.0 - - - +
116B PHE* 4.0 16.9 - - + -
153B SER* 5.4 1.1 - - - +
154B PRO* 3.6 23.8 - - + -
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Residues in contact with CYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR 3.8 4.9 - - - -
18B ILE* 1.3 76.8 - - - +
20B HIS* 1.3 59.3 + - - +
21B LEU* 4.0 8.7 - - + -
33B TYR* 3.2 11.9 - - - -
34B GLY 2.8 34.5 + - - +
36B GLY 4.4 4.9 - - - -
41B ILE* 4.3 13.7 - - + -
57B VAL* 4.2 15.0 - - + -
58B GLN 3.2 9.2 - - - +
59B SER* 3.8 6.7 - - - -
94B PHE* 3.1 41.1 - - - -
116B PHE* 4.8 0.9 - - - -
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Residues in contact with HIS 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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19B CYS* 1.3 73.3 - - - +
21B LEU* 1.3 60.9 + - - +
22B THR* 3.5 22.0 + - - -
31B SER* 3.9 25.2 + - - -
32B LEU* 3.6 11.6 + - - -
33B TYR* 3.3 42.6 + + + -
56B LEU 3.4 4.7 - - - +
57B VAL* 3.6 1.6 - - - -
58B GLN* 2.8 45.8 + - + +
116B PHE* 4.1 14.5 - + + -
149B GLY 5.1 1.0 + - - -
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Residues in contact with LEU 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 CYS* 4.2 8.5 - - + -
20B HIS* 1.3 80.0 - - - +
22B THR* 1.3 64.0 + - - +
23B ASN 4.2 0.7 - - - -
30B THR 3.7 0.6 - - - +
31B SER* 3.0 6.1 - - - -
32B LEU* 2.6 49.2 + - + +
34B GLY* 4.2 8.5 - - - +
41B ILE* 4.1 17.0 - - + -
43B THR* 3.6 40.2 - - + +
47B LEU* 4.2 10.1 - - + -
55B LEU* 4.2 13.2 - - + -
56B LEU 3.4 1.8 - - - -
57B VAL* 3.7 34.3 - - + -
85B ILE* 5.0 2.7 - - + -
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B HIS* 3.5 19.9 + - - -
21B LEU* 1.3 78.4 + - - +
23B ASN* 1.3 61.6 + - - +
24B GLU* 3.6 6.9 + - + +
29B THR* 4.4 20.0 - - + -
30B THR 3.5 5.6 - - - +
31B SER* 4.3 9.0 - - - +
54B THR* 3.4 2.3 + - - +
55B LEU* 3.4 6.1 - - - +
56B LEU* 2.9 57.2 + - + +
310D THR 5.8 0.7 - - - +
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Residues in contact with ASN 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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21B LEU 4.2 0.2 - - - -
22B THR* 1.3 70.3 - - - +
24B GLU* 1.3 59.9 + - - +
25B SER* 3.0 24.3 + - - -
28B HIS 3.5 1.0 - - - +
29B THR* 2.9 8.5 - - - -
30B THR* 2.7 37.1 + - - +
47B LEU* 2.9 41.2 + - + +
48B PHE* 3.8 16.4 - - - -
50B ARG* 3.1 24.0 + - - +
51B ASN* 4.8 0.8 - - - +
54B THR 3.5 7.7 - - - +
55B LEU* 4.1 6.0 - - + +
69B THR* 4.4 8.1 - - - +
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Residues in contact with GLU 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 THR* 3.6 8.6 + - + +
23B ASN* 1.3 69.8 + - - +
25B SER* 1.3 62.4 + - - +
27B GLY* 4.1 7.3 + - - -
28B HIS 2.8 30.6 + - - +
29B THR* 3.0 22.1 - - + +
53B GLY* 3.1 3.5 - - - -
54B THR* 2.9 49.8 + - - +
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Residues in contact with SER 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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23B ASN* 3.0 19.3 + - - -
24B GLU* 1.3 71.0 + - - +
26B ASP* 1.3 64.5 + - - +
27B GLY 3.2 2.5 - - - -
28B HIS* 2.7 42.0 + - - +
50B ARG* 3.7 28.1 - - - -
51B ASN 4.2 0.7 + - - -
52B ASN 3.2 18.9 + - - -
53B GLY* 3.0 20.5 + - - -
69B THR* 4.4 0.2 + - - -
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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