Contacts of the helix formed by residues 15 - 23 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G GLY* 3.0 20.2 + - - +
140G PHE* 3.8 19.7 - - + -
158G ILE* 3.9 22.0 - - + -
14I SER* 1.3 75.5 + - - +
16I ALA* 1.3 58.1 + - - +
17I PRO* 3.5 1.8 - - - -
18I MET* 3.3 15.9 + - + +
19I LEU* 3.0 36.0 + - + +
142I VAL* 3.8 25.8 - - + -
156I SER* 3.9 17.3 - - - +
194I LEU* 3.6 30.1 - - + +
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Residues in contact with ALA 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ARG* 3.6 29.6 - - + +
137G VAL 3.2 23.7 - - - +
138G GLY* 3.6 3.0 - - - -
139G ASP* 3.5 11.7 - - - +
14I SER* 3.1 16.2 + - - +
15I LEU* 1.3 72.4 - - - +
17I PRO* 1.4 67.2 - - + +
19I LEU* 4.3 0.2 - - - -
20I GLU* 2.9 28.1 + - - +
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Residues in contact with PRO 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ARG* 4.2 14.3 - - - +
14I SER* 3.6 23.3 - - - +
15I LEU 3.6 0.9 - - - -
16I ALA* 1.4 93.5 - - + +
18I MET* 1.4 58.8 + - - +
20I GLU* 3.6 23.1 - - - +
21I LYS* 3.6 20.8 - - - +
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Residues in contact with MET 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 3.3 18.7 + - + +
17I PRO* 1.4 78.2 - - - +
19I LEU* 1.4 94.4 + - + +
21I LYS* 3.5 11.9 + - - +
22I VAL* 3.4 20.7 + - - +
142I VAL* 4.2 19.5 - - + -
192I LEU* 4.7 2.7 - - + -
193I ASN 3.3 25.8 - - - +
194I LEU* 3.4 24.2 - - + +
195I ASN* 4.6 7.4 - - - +
196I GLY* 3.5 20.9 - - - +
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G VAL* 3.9 12.8 - - + +
138G GLY* 3.7 25.6 - - - +
158G ILE* 5.0 0.7 - - + -
15I LEU* 3.0 31.8 + - + +
16I ALA 3.3 3.3 + - - +
18I MET* 1.4 96.2 - - + +
20I GLU* 1.4 60.5 + - - +
22I VAL* 3.0 4.0 + - + -
23I LEU* 2.8 64.3 + - + +
142I VAL* 4.2 22.9 - - + -
144I VAL* 4.6 0.9 - - + -
154I ALA* 4.5 7.9 - - + -
192I LEU* 4.5 10.5 - - + -
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Residues in contact with GLU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ARG* 3.0 46.2 + - - -
16I ALA 2.9 13.0 + - - +
17I PRO* 3.6 12.8 - - - +
19I LEU* 1.4 75.8 - - - +
21I LYS* 1.3 61.0 + - + +
23I LEU* 4.8 4.2 - - - +
24I PRO* 3.7 15.6 - - - +
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Residues in contact with LYS 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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17I PRO* 3.6 24.0 - - - +
18I MET* 3.5 9.6 + - + +
19I LEU 3.2 0.6 - - - -
20I GLU* 1.3 75.8 - - + +
22I VAL* 1.3 65.5 + - + +
24I PRO* 3.8 8.4 - - - +
125I THR* 3.9 14.9 - - - +
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I MET* 3.4 20.4 - - - +
19I LEU* 3.0 4.6 + - + +
21I LYS* 1.3 82.1 - - + +
23I LEU* 1.3 66.8 + - + +
24I PRO* 3.3 3.6 - - - -
25I ALA* 3.0 24.4 + - - +
26I VAL* 4.1 4.2 + - + +
125I THR* 5.3 0.9 - - - -
127I ILE* 4.2 9.9 - - + -
192I LEU* 3.5 32.5 - - + -
195I ASN 4.5 4.5 - - - +
196I GLY* 3.4 32.5 - - - +
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Residues in contact with LEU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G VAL* 4.1 28.3 - - + -
19I LEU* 2.8 44.3 + - + +
20I GLU* 4.8 3.4 - - - +
22I VAL* 1.3 71.9 - - + +
24I PRO* 1.4 65.0 - - + +
26I VAL* 3.0 12.6 + - - +
95I ASN* 3.5 8.6 + - - +
144I VAL* 3.7 33.9 - - + -
152I GLN* 2.9 45.8 - - + +
154I ALA* 4.8 5.2 - - + -
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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
------------------------------------------------------------
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