Contacts of the strand formed by residues 16 - 21 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F GLY* 3.0 19.3 + - - -
14F SER 3.7 0.4 - - - -
15F GLY* 1.3 87.2 - - - +
17F CYS* 1.3 57.1 + - - +
18F LYS* 2.9 32.7 + - + +
30F VAL* 3.5 28.3 - - + +
31F PHE* 3.5 23.3 - - - +
32F PRO* 4.1 12.8 - - + -
33F SER* 3.7 5.4 - - - -
210F ARG* 4.8 10.3 - - - +
336F LYS* 4.3 13.5 - - - +
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Residues in contact with CYS 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 5.9 3.6 - - + -
11F ASP 3.3 13.0 - - - +
12F ASN* 4.3 12.8 - - - -
16F MET* 1.3 74.0 - - - +
18F LYS* 1.3 63.0 + - - +
19F ALA* 6.1 0.4 - - + -
29F ALA 3.7 0.6 - - - +
30F VAL* 3.3 3.5 - - - +
31F PHE* 2.8 56.8 + - + -
33F SER* 3.0 24.7 - - - -
71F ILE* 4.4 7.2 - - - -
85F ILE* 3.9 27.4 - - - -
89F THR* 5.7 0.2 - - - -
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Residues in contact with LYS 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 5.0 0.3 - - - +
11F ASP* 2.8 62.7 + - + +
13F GLY* 4.4 5.5 - - - -
16F MET* 2.9 32.1 + - + +
17F CYS* 1.3 77.1 - - - +
19F ALA* 1.3 58.3 + - - +
27F PRO* 3.6 22.7 - - + -
29F ALA 3.2 6.3 - - - -
30F VAL* 4.0 8.1 - - + -
336F LYS* 3.5 28.3 - - - +
337F TYR* 3.9 21.1 - - + -
340F TRP* 3.3 18.3 - - + -
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL 3.2 10.3 - - - +
10F VAL* 4.4 5.2 - - + -
17F CYS* 6.1 0.4 - - + -
18F LYS* 1.3 75.6 - - - +
20F GLY* 1.3 58.0 + - - +
27F PRO* 4.3 0.6 - - - +
28F ARG 3.1 4.5 + - - -
29F ALA* 3.0 36.1 + - + +
31F PHE* 4.9 4.3 - - + -
89F THR* 3.7 20.2 - - + -
94F LEU* 3.6 27.1 - - + +
340F TRP* 3.7 3.6 - - - +
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Residues in contact with GLY 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.1 11.1 - - - +
9F VAL 2.9 26.0 + - - -
19F ALA* 1.3 77.8 - - - +
21F PHE* 1.3 68.7 + - - -
26F ALA 5.4 0.2 - - - -
28F ARG* 4.2 9.0 - - - -
94F LEU* 3.9 11.5 - - - +
340F TRP* 3.4 17.1 - - - +
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Residues in contact with PHE 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ASP* 3.4 33.9 - - - -
4F ASP* 5.9 0.7 - - - -
6F ALA* 4.5 6.3 - - + -
7F ALA 3.6 3.4 - - - +
8F LEU* 3.2 35.7 - - + -
9F VAL* 4.7 0.7 - - - -
20F GLY* 1.3 77.9 - - - -
22F ALA* 1.3 68.5 + - - +
24F ASP* 3.1 37.1 + - - +
28F ARG* 3.3 40.8 - - - +
94F LEU* 4.3 26.7 - - + -
96F VAL* 3.8 21.5 - - + -
101F HIS* 5.3 0.9 - + - -
340F TRP* 3.8 8.7 - - - -
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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