Contacts of the helix formed by residues 16 - 28 (chain V) in PDB entry 3A68
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 GLU 16 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115E VAL* 4.2 26.2 - - + +
14V ILE 6.1 0.7 - - - +
15V PHE* 1.3 82.5 - - - +
17V PRO* 1.3 70.9 - - + +
18V PHE* 3.3 1.6 - - + +
19V GLU* 3.0 39.0 + - + +
20V GLU* 3.0 16.9 + - - +
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Residues in contact with PRO 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ASN* 3.6 23.8 - - + +
59E VAL* 5.9 0.9 - - + -
62E VAL* 4.0 24.0 - - + -
115E VAL* 4.0 10.5 - - + -
117E PRO* 6.2 0.4 - - + -
139E LEU* 4.0 20.9 - - + -
142E LEU* 4.0 2.5 - - + +
15V PHE* 3.6 35.6 - - + +
16V GLU* 1.3 82.8 - - - +
18V PHE* 1.3 64.0 + - + +
20V GLU 3.4 0.3 + - - -
21V VAL* 2.8 37.0 + - - +
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Residues in contact with PHE 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E VAL* 3.7 34.8 - - + -
115E VAL* 6.1 0.9 - - + -
116E MET 5.0 2.7 - - - -
117E PRO* 3.6 13.7 - - + -
118E LEU* 3.2 68.0 - - + -
121E PHE* 4.2 6.5 - + - -
135E LEU* 3.6 33.4 - - + -
139E LEU* 5.8 1.8 - - + -
16V GLU* 3.3 1.6 - - + +
17V PRO* 1.3 89.7 - - + +
19V GLU* 1.3 62.2 + - - +
21V VAL* 3.4 10.3 - - + +
22V LYS* 3.2 25.9 - - - +
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Residues in contact with GLU 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V GLU* 3.0 37.0 + - + +
18V PHE* 1.3 81.6 - - + +
20V GLU* 1.3 67.8 + - + +
22V LYS* 2.9 54.7 + - - +
23V LYS 4.7 0.2 + - - -
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Residues in contact with GLU 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 3.8 22.8 - - + +
146E LYS* 3.0 35.7 + - - -
14V ILE 4.7 1.2 - - - +
15V PHE* 3.1 36.4 - - - +
16V GLU 3.0 14.2 + - - +
19V GLU* 1.3 78.4 - - + +
21V VAL* 1.3 61.8 + - - +
22V LYS 3.2 0.6 + - - -
23V LYS* 3.7 20.6 + - - +
24V GLU* 4.3 1.6 + - - +
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Residues in contact with VAL 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E LEU* 4.2 19.5 - - + -
138E SER* 3.4 41.7 - - - +
139E LEU* 3.8 15.5 - - + +
142E LEU* 4.0 9.1 - - + +
17V PRO 2.8 21.6 + - - +
18V PHE* 3.4 21.3 - - + +
20V GLU* 1.3 75.9 - - - +
22V LYS* 1.3 67.8 + - - +
23V LYS 3.2 0.2 - - - -
24V GLU* 2.9 7.5 + - + +
25V LEU* 2.8 27.0 + - + +
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Residues in contact with LYS 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V PHE 3.2 19.7 - - - +
19V GLU* 2.9 44.4 + - - +
20V GLU 3.2 0.4 - - - -
21V VAL* 1.3 78.8 - - + +
23V LYS* 1.3 65.7 + - - +
25V LEU* 3.1 20.3 + - + +
26V ASP* 3.3 20.5 + - - +
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Residues in contact with LYS 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 6.4 1.1 - - + -
145E GLU* 3.1 37.7 + - - +
19V GLU 4.7 0.4 + - - -
20V GLU 3.7 13.1 + - - +
22V LYS* 1.3 79.5 - - - +
24V GLU* 1.3 68.0 + - - +
26V ASP* 3.5 3.9 + - - +
27V LEU* 3.0 44.8 + - + +
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Residues in contact with GLU 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E SER* 3.5 34.5 - - - +
141E LYS* 3.6 34.5 + - + +
142E LEU* 4.4 6.6 + - + +
145E GLU* 2.6 29.9 - - - +
20V GLU 4.3 1.1 + - - +
21V VAL* 2.9 13.2 + - + +
23V LYS* 1.3 87.0 + - - +
25V LEU* 1.3 67.3 + - - +
27V LEU* 3.0 33.4 + - - +
28V VAL* 3.3 10.3 + - + +
39V GLN* 4.5 5.1 + - - +
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Residues in contact with LEU 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E HIS* 5.8 10.3 - - + +
134E GLU* 4.1 16.2 - - + +
135E LEU* 4.2 23.6 - - + +
138E SER* 3.3 23.3 + - - +
21V VAL* 2.8 23.5 + - + +
22V LYS* 3.5 16.2 - - + +
24V GLU* 1.3 77.5 - - - +
26V ASP* 1.3 66.3 + - - +
27V LEU 3.2 0.5 + - - -
28V VAL* 3.3 21.9 + - + +
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Residues in contact with ASP 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V LYS* 3.3 13.9 + - - +
23V LYS* 4.0 7.4 - - - +
24V GLU 3.3 0.2 - - - -
25V LEU* 1.3 80.7 - - - +
27V LEU* 1.3 66.7 + - + +
28V VAL 3.3 5.1 + - - +
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Residues in contact with LEU 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E LYS* 5.8 2.9 + - - +
23V LYS* 3.0 37.0 - - + +
24V GLU* 3.0 30.4 + - - +
26V ASP* 1.3 84.5 - - + +
28V VAL* 1.3 64.4 + - - +
29V PRO* 3.0 11.4 - - - +
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Residues in contact with VAL 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E GLU* 4.6 22.2 - - + +
137E LEU* 4.7 17.9 - - + -
138E SER* 3.6 22.9 - - - +
141E LYS* 5.9 5.4 - - + +
185E VAL* 5.5 0.4 - - + -
189E ARG* 3.6 24.0 - - - +
24V GLU* 3.3 5.9 + - + +
25V LEU* 3.3 19.4 + - + +
26V ASP 4.1 5.7 - - - +
27V LEU* 1.3 75.2 - - - +
29V PRO* 1.3 73.9 - - + +
30V THR* 3.7 10.7 + - - +
36V LEU* 4.1 8.3 - - + -
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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