Contacts of the helix formed by residues 15 - 23 (chain L) in PDB entry 3STJ
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 LEU 15 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138J GLY* 2.9 21.2 + - - +
140J PHE* 3.9 19.1 - - + -
158J ILE* 3.9 23.6 - - + -
14L SER* 1.3 74.8 - - - +
16L ALA* 1.4 54.3 + - - +
17L PRO* 3.5 1.8 - - - -
18L MET* 3.3 17.9 + - + +
19L LEU* 2.9 39.1 + - + +
142L VAL* 3.8 23.3 - - + -
156L SER* 3.9 17.7 - - - +
194L LEU* 3.6 29.8 - - + -
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Residues in contact with ALA 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ARG* 3.6 37.7 - - + +
137J VAL 3.2 24.9 - - - +
138J GLY* 3.6 3.4 - - - -
139J ASP* 3.7 2.7 - - - +
14L SER* 3.0 16.8 + - - +
15L LEU* 1.4 73.1 - - - +
17L PRO* 1.4 68.0 - - + +
19L LEU* 3.9 0.6 - - - +
20L GLU* 2.9 28.0 + - + +
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Residues in contact with PRO 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J ARG* 4.0 15.2 - - - +
14L SER* 3.6 24.2 - - - +
15L LEU 3.6 0.9 - - - -
16L ALA* 1.4 93.3 - - + +
18L MET* 1.4 59.4 + - - +
20L GLU* 3.9 18.0 + - - +
21L LYS* 3.7 26.6 - - - +
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Residues in contact with MET 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L LEU* 3.3 19.6 + - + +
16L ALA 3.3 0.2 - - - -
17L PRO* 1.4 77.2 - - - +
19L LEU* 1.4 88.8 + - + +
21L LYS* 3.4 20.1 + - - +
22L VAL* 3.5 18.3 + - - +
142L VAL* 3.8 27.1 - - + -
192L LEU* 4.7 2.5 - - + -
193L ASN 3.4 21.3 - - - +
194L LEU* 3.6 24.0 - - + +
195L ASN* 4.8 6.3 - - - +
196L GLY* 3.5 25.1 - - - -
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Residues in contact with LEU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J VAL* 3.8 13.5 - - + +
138J GLY* 3.7 30.1 - - - +
158J ILE* 4.9 1.6 - - + -
15L LEU* 2.9 21.9 + - + +
16L ALA 3.1 3.1 + - - +
18L MET* 1.4 100.5 - - + +
20L GLU* 1.4 56.2 + - - +
21L LYS 3.2 0.5 + - - -
22L VAL* 3.2 1.7 + - + -
23L LEU* 2.8 63.4 + - + +
142L VAL* 4.1 18.2 - - + -
144L VAL* 4.5 0.9 - - + -
154L ALA* 4.1 18.6 - - + -
192L LEU* 4.2 11.7 - - + -
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Residues in contact with GLU 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ARG* 3.1 44.2 + - + +
137J VAL 5.5 0.2 + - - -
16L ALA* 2.9 15.2 + - - +
17L PRO* 3.9 12.3 - - - +
18L MET 3.4 0.2 - - - -
19L LEU* 1.4 74.1 - - - +
21L LYS* 1.3 61.9 + - + +
23L LEU* 5.2 4.3 - - - -
24L PRO* 3.9 14.1 - - - +
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Residues in contact with LYS 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L PRO* 3.7 23.6 - - - +
18L MET* 3.4 9.6 + - - +
19L LEU 3.2 0.8 - - - -
20L GLU* 1.3 78.9 - - + +
22L VAL* 1.3 65.9 + - + +
24L PRO* 4.0 3.8 - - - +
125L THR* 3.9 19.2 - - - +
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Residues in contact with VAL 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L MET* 3.5 16.4 - - - +
19L LEU* 3.2 3.8 + - + +
21L LYS* 1.3 84.1 - - + +
23L LEU* 1.4 61.5 + - - +
24L PRO* 3.3 3.4 - - - -
25L ALA* 2.9 32.0 + - - +
26L VAL* 4.1 3.8 + - + +
125L THR* 5.3 0.2 - - - -
126L GLN 6.0 0.9 - - - +
127L ILE* 4.3 10.5 - - + -
128L ALA* 6.0 1.1 - - + +
192L LEU* 3.5 32.8 - - + -
195L ASN 4.6 4.0 - - - +
196L GLY* 3.3 35.0 - - - +
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Residues in contact with LEU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J VAL* 4.1 28.5 - - + +
19L LEU* 2.8 55.0 + - + +
20L GLU* 4.9 3.1 - - - +
22L VAL* 1.4 71.3 - - + +
24L PRO* 1.4 65.3 - - + +
26L VAL* 3.0 14.0 + - - +
95L ASN* 3.5 8.7 - - - +
144L VAL* 3.7 26.0 - - + -
152L GLN* 2.9 43.6 - - + +
154L ALA* 4.7 7.4 - - + -
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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