Contacts of the helix formed by residues 15 - 23 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G SER* 1.3 75.3 + - - +
16G ALA* 1.4 58.4 + - - +
17G PRO* 3.5 2.0 - - - -
18G MET* 3.4 16.4 + - + +
19G LEU* 2.9 40.6 + - + +
142G VAL* 3.7 25.4 - - + -
156G SER* 3.9 17.3 - - - +
194G LEU* 3.6 28.5 - - + -
138H GLY 3.1 11.1 + - - +
140H PHE* 3.8 23.1 - - + -
158H ILE* 4.0 22.0 - - + -
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Residues in contact with ALA 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G SER* 3.0 17.7 + - - +
15G LEU* 1.4 73.1 - - - +
17G PRO* 1.4 66.3 - - + +
19G LEU 4.4 0.4 - - - +
20G GLU* 2.9 27.4 + - - +
136H ARG* 3.6 28.3 - - + +
137H VAL 3.2 25.3 - - - +
138H GLY* 3.6 2.4 - - - -
139H ASP* 3.6 12.1 - - - +
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Residues in contact with PRO 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G SER* 3.6 23.8 - - - +
15G LEU 3.6 1.1 - - - -
16G ALA* 1.4 93.6 - - + +
18G MET* 1.4 60.0 + - - +
20G GLU* 3.6 23.0 - - - +
21G LYS* 3.6 18.4 - - - +
136H ARG* 4.1 14.8 - - - +
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Residues in contact with MET 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 3.4 18.0 + - + +
16G ALA 3.3 0.2 - - - -
17G PRO* 1.4 79.2 - - - +
19G LEU* 1.3 93.3 + - + +
21G LYS* 3.4 28.1 + - - +
22G VAL* 3.4 20.4 + - + +
142G VAL* 4.1 19.5 - - + -
192G LEU* 5.0 1.8 - - + -
193G ASN 3.5 20.0 - - - +
194G LEU* 3.5 24.0 - - + +
195G ASN* 4.7 7.0 - - - +
196G GLY* 3.4 24.9 - - - -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 2.9 31.4 + - + +
16G ALA 3.2 2.7 + - - +
18G MET* 1.3 95.5 - - + +
20G GLU* 1.3 59.6 + - - +
22G VAL* 3.1 3.2 + - + +
23G LEU* 2.8 65.3 + - + +
142G VAL* 4.1 24.5 - - + -
144G VAL* 4.3 0.7 - - + -
154G ALA* 4.5 10.5 - - + -
192G LEU* 4.3 12.1 - - + -
137H VAL* 4.0 8.3 - - + +
138H GLY* 3.6 26.7 - - - +
158H ILE* 5.1 0.7 - - + -
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Residues in contact with GLU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ALA 2.9 13.1 + - - +
17G PRO* 3.6 12.4 - - - +
19G LEU* 1.3 76.5 - - - +
21G LYS* 1.3 59.1 + - + +
23G LEU* 4.6 4.7 - - - +
24G PRO* 3.7 16.1 - - - +
136H ARG* 3.1 45.2 + - - -
137H VAL 5.5 0.4 + - - -
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Residues in contact with LYS 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G PRO* 3.6 22.4 - - - +
18G MET* 3.7 20.4 - - - +
19G LEU 3.2 0.6 - - - -
20G GLU* 1.3 76.7 - - + +
22G VAL* 1.3 65.7 + - + +
24G PRO* 3.8 4.3 - - - +
125G THR* 3.8 20.1 - - - +
195G ASN 5.3 5.3 + - - -
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Residues in contact with VAL 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G MET* 3.4 17.9 + - + +
19G LEU* 3.1 4.2 + - + +
21G LYS* 1.3 82.6 - - + +
23G LEU* 1.4 67.7 + - - +
24G PRO* 3.3 2.9 - - - -
25G ALA* 2.8 27.3 + - - +
26G VAL* 4.0 4.0 + - + +
125G THR* 5.2 0.9 - - - -
126G GLN 6.1 0.2 - - - -
127G ILE* 3.7 13.0 - - + -
192G LEU* 3.6 26.2 - - + -
195G ASN 4.6 3.8 - - - +
196G GLY* 3.4 38.4 - - - +
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Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 2.8 50.3 + - + +
20G GLU* 4.6 3.4 - - - +
22G VAL* 1.4 72.2 - - - +
24G PRO* 1.4 65.5 - - + +
26G VAL* 2.9 18.0 + - - +
95G ASN* 3.7 5.8 - - - +
144G VAL* 3.6 39.5 - - + -
152G GLN* 3.0 36.1 - - + +
154G ALA* 4.6 7.4 - - + -
192G LEU* 5.8 0.2 - - + -
137H VAL* 4.2 22.9 - - + +
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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
------------------------------------------------------------
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