Contacts of the strand formed by residues 16 - 21 (chain I) in PDB entry 3LUE
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 MET 16 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I GLY* 3.0 19.0 + - - -
14I SER 3.7 0.4 - - - -
15I GLY* 1.3 88.9 - - - +
17I CYS* 1.3 57.7 + - - +
18I LYS* 2.9 32.5 + - + +
30I VAL* 3.5 28.5 - - + +
31I PHE* 3.5 23.1 - - - +
32I PRO* 4.1 11.9 - - + -
33I SER* 3.7 5.4 - - - -
210I ARG* 4.8 10.3 - - - +
336I LYS* 4.3 12.8 - - - +
337I TYR* 5.5 0.4 - - - +
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Residues in contact with CYS 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I VAL* 5.9 3.4 - - + -
11I ASP 3.3 12.8 - - - +
12I ASN* 4.3 11.7 - - - -
16I MET* 1.3 74.2 - - - +
18I LYS* 1.3 63.3 + - - +
19I ALA* 6.1 0.4 - - + -
29I ALA 3.7 1.1 - - - +
30I VAL* 3.3 3.6 - - - +
31I PHE* 2.8 56.4 + - + -
33I SER* 3.0 24.7 - - - -
71I ILE* 4.4 8.1 - - - -
85I ILE* 3.9 27.6 - - - -
89I THR* 5.7 0.4 - - - +
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Residues in contact with LYS 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I VAL* 5.0 0.3 - - - +
11I ASP* 2.8 60.8 + - + +
13I GLY* 4.4 6.3 - - - -
16I MET* 2.9 31.3 + - + +
17I CYS* 1.3 78.3 - - - +
19I ALA* 1.3 59.1 + - - +
27I PRO* 3.6 22.7 - - + -
29I ALA 3.2 5.8 - - - -
30I VAL* 4.0 8.7 - - + +
336I LYS* 3.5 27.6 - - - +
337I TYR* 3.9 21.8 - - + -
340I TRP* 3.3 18.4 - - + -
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Residues in contact with ALA 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL 3.2 9.2 - - - +
10I VAL* 4.4 5.2 - - + -
17I CYS* 6.1 0.7 - - + -
18I LYS* 1.3 75.4 - - - +
20I GLY* 1.3 59.0 + - - +
27I PRO* 4.3 0.6 - - - +
28I ARG 3.1 4.7 + - - -
29I ALA* 3.0 36.5 + - + +
31I PHE* 4.9 4.7 - - + -
89I THR* 3.7 20.4 - - + -
94I LEU* 3.6 26.2 - - + +
340I TRP* 3.7 3.6 - - - +
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Residues in contact with GLY 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 3.1 10.9 - - - +
9I VAL 2.9 26.1 + - - -
19I ALA* 1.3 76.4 - - - +
21I PHE* 1.3 68.4 + - - -
28I ARG* 4.2 9.2 - - - -
94I LEU* 3.9 12.3 - - - +
340I TRP* 3.4 17.0 - - - +
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Residues in contact with PHE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ASP* 3.4 33.4 - - - +
4I ASP* 5.9 1.1 - - - -
6I ALA* 4.5 7.4 - - + -
7I ALA 3.6 3.1 - - - +
8I LEU* 3.2 34.8 - - + -
20I GLY* 1.3 78.6 - - - -
22I ALA* 1.3 69.7 + - - +
24I ASP* 3.1 37.2 + - - +
28I ARG* 3.3 41.3 - - - +
94I LEU* 4.3 26.7 - - + -
96I VAL* 3.8 21.8 - - + -
101I HIS* 5.3 1.3 - + - -
340I TRP* 3.8 9.0 - - - -
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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