Contacts of the helix formed by residues 15 - 23 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLY* 2.9 22.9 + - - +
140D PHE* 3.8 19.3 - - + -
158D ILE* 3.9 28.7 - - + -
14F SER* 1.3 73.8 - - - +
16F ALA* 1.4 58.4 + - - +
17F PRO* 3.5 2.0 - - - -
18F MET* 3.3 19.3 + - + +
19F LEU* 3.0 32.4 + - + +
142F VAL* 3.8 24.0 - - + -
156F SER* 3.9 11.7 - - - +
194F LEU* 3.6 28.7 - - + -
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Residues in contact with ALA 16 (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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136D ARG* 3.6 29.6 - - + +
137D VAL 3.2 23.3 - - - +
138D GLY* 3.6 2.8 - - - -
139D ASP* 3.5 11.7 - - - +
14F SER* 3.0 17.3 + - - +
15F LEU* 1.4 73.7 - - - +
17F PRO* 1.4 66.8 - - + +
19F LEU 3.0 0.4 + - - +
20F GLU* 2.9 28.1 + - - +
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Residues in contact with PRO 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ARG* 3.9 21.7 - - - +
14F SER* 3.6 24.7 - - - +
15F LEU 3.6 1.1 - - - -
16F ALA* 1.4 92.4 - - + +
18F MET* 1.4 58.0 + - - +
20F GLU* 3.6 15.8 - - - +
21F LYS* 3.6 20.1 - - - +
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Residues in contact with MET 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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15F LEU* 3.3 21.7 + - + +
16F ALA 3.2 0.2 - - - -
17F PRO* 1.4 76.3 - - - +
19F LEU* 1.3 86.7 + - + +
20F GLU 3.3 0.2 - - - -
21F LYS* 3.8 13.5 + - - +
22F VAL* 3.4 21.8 + - + +
142F VAL* 3.9 21.8 - - + -
192F LEU* 4.9 2.0 - - + -
193F ASN 3.3 20.9 - - - +
194F LEU* 3.6 23.3 - - + +
195F ASN* 4.8 6.1 - - - +
196F GLY* 3.3 29.6 - - - -
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D VAL* 3.9 11.7 - - + +
138D GLY* 3.7 29.2 - - - +
158D ILE* 5.0 0.9 - - + -
15F LEU* 3.0 23.3 + - + +
16F ALA 3.0 0.8 + - - +
18F MET* 1.3 98.2 - - + +
20F GLU* 1.3 63.1 + - - +
22F VAL* 3.0 2.9 + - + +
23F LEU* 2.8 63.2 + - + +
142F VAL* 4.1 19.1 - - + -
144F VAL* 4.5 0.4 - - + -
154F ALA* 4.3 17.5 - - + -
192F LEU* 4.3 12.6 - - + -
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Residues in contact with GLU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ARG* 2.8 46.4 + - - -
16F ALA 2.9 12.6 + - - +
17F PRO* 3.6 12.7 - - - +
19F LEU* 1.3 77.3 - - - +
21F LYS* 1.3 59.5 + - + +
23F LEU* 4.7 3.3 - - - +
24F PRO* 3.9 13.7 - - - +
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Residues in contact with LYS 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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17F PRO* 3.6 24.5 - - - +
18F MET* 4.0 11.4 - - - +
19F LEU 3.2 0.4 - - - -
20F GLU* 1.3 76.8 - - + +
22F VAL* 1.3 66.7 + - + +
24F PRO* 3.9 4.3 - - - +
125F THR* 3.8 19.9 - - - +
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Residues in contact with VAL 22 (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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18F MET 3.4 17.3 - - - +
19F LEU* 3.0 6.3 + - + +
21F LYS* 1.3 81.7 - - + +
23F LEU* 1.3 67.7 + - + +
24F PRO* 3.3 3.8 - - - -
25F ALA* 3.1 23.6 + - - +
26F VAL* 4.2 4.3 + - + +
125F THR* 5.2 0.9 - - - -
126F GLN 6.1 0.9 - - - +
127F ILE* 3.8 13.5 - - + -
192F LEU* 3.6 31.0 - - + -
195F ASN 4.6 3.6 - - - +
196F GLY* 3.3 32.1 - - - +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D VAL* 3.9 22.9 - - + +
19F LEU* 2.8 50.3 + - + +
20F GLU* 4.7 2.2 - - - +
22F VAL* 1.3 70.7 - - - +
24F PRO* 1.4 65.5 - - + +
26F VAL* 3.0 16.9 + - - +
95F ASN* 3.5 5.8 - - - +
144F VAL* 3.6 38.4 - - + -
152F GLN* 2.9 42.6 - - + +
154F ALA* 4.6 7.9 - - + -
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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