Contacts of the helix formed by residues 16 - 28 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15K PHE* 1.3 80.3 - - - +
17K PRO* 1.3 70.4 - - - +
18K PHE 3.3 2.2 - - - +
19K GLU* 3.1 47.0 + - + +
20K GLU* 3.2 19.6 + - - +
115P VAL* 4.2 20.1 - - + +
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Residues in contact with PRO 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K PHE* 3.3 41.5 - - + +
16K GLU* 1.3 84.4 - - - +
18K PHE* 1.3 62.7 + - + +
20K GLU* 3.5 1.2 + - - +
21K VAL* 2.9 36.3 + - - +
58P ASN* 3.8 17.5 - - + +
59P VAL* 5.2 0.7 - - + +
62P VAL* 4.0 26.7 - - + -
115P VAL* 3.6 18.4 - - + -
139P LEU* 4.1 12.8 - - + -
142P LEU* 4.7 0.7 - - + -
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Residues in contact with PHE 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K GLU* 3.3 1.2 - - - +
17K PRO* 1.3 84.8 - - + +
19K GLU* 1.3 67.5 + - + +
20K GLU 3.4 0.2 - - - -
21K VAL* 3.9 7.8 - - + +
22K LYS* 3.4 21.8 + - - +
62P VAL* 3.6 37.0 - - + -
115P VAL* 6.0 1.3 - - + -
116P MET 4.9 3.1 - - - -
117P PRO* 3.6 13.5 - - + -
118P LEU* 3.1 65.7 - - + -
121P PHE* 4.3 12.1 - + - -
135P LEU* 4.8 18.4 - - + -
139P LEU* 5.7 4.7 - - + -
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Residues in contact with GLU 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K GLU* 3.1 43.7 + - + +
18K PHE* 1.3 81.0 - - + +
20K GLU* 1.3 59.6 + - - +
22K LYS* 3.2 37.0 + - - +
23K LYS* 5.0 2.8 - - - +
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Residues in contact with GLU 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K PHE* 3.1 22.5 - - - -
16K GLU 3.2 15.2 + - - +
17K PRO 4.0 0.2 - - - +
19K GLU* 1.3 78.9 - - + +
21K VAL* 1.3 60.1 - - - +
22K LYS 3.6 0.2 - - - -
23K LYS* 4.2 5.2 + - - +
24K GLU* 3.9 14.4 + - - +
142P LEU* 3.7 29.2 - - + +
146P LYS* 2.9 28.0 + - - -
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Residues in contact with VAL 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K PRO 2.9 24.5 + - - +
18K PHE* 3.9 9.8 - - + +
19K GLU 3.3 0.2 - - - -
20K GLU* 1.3 76.4 - - - +
22K LYS* 1.3 59.2 + - - +
23K LYS 3.0 2.9 - - - -
24K GLU* 2.8 4.7 + - - -
25K LEU* 2.6 35.2 + - + +
135P LEU* 3.9 29.4 - - + +
138P SER* 3.9 16.2 - - - +
139P LEU* 3.5 39.0 - - + +
142P LEU* 3.9 13.0 - - + -
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Residues in contact with LYS 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K PHE 3.4 14.1 + - - +
19K GLU* 3.2 28.1 + - - +
21K VAL* 1.3 80.2 - - - +
23K LYS* 1.3 92.2 + - + +
25K LEU* 3.8 10.0 + - - +
26K ASP* 2.9 29.6 + - - +
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Residues in contact with LYS 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K GLU 5.0 3.1 - - - +
20K GLU 4.2 6.2 + - - +
21K VAL 3.0 0.6 - - - -
22K LYS* 1.3 107.6 - - + +
24K GLU* 1.3 66.5 + - - +
25K LEU 3.2 0.2 - - - -
26K ASP* 3.2 20.1 + - - +
27K LEU* 3.4 18.6 + - - +
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Residues in contact with GLU 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K GLU 3.9 6.1 + - - +
21K VAL* 2.8 19.3 + - + +
23K LYS* 1.3 78.4 - - - +
25K LEU* 1.3 58.5 + - - +
27K LEU* 3.0 44.1 + - - +
28K VAL* 3.6 6.2 + - - +
39K GLN* 4.8 5.1 + - - +
138P SER* 3.4 35.2 + - - +
141P LYS* 3.8 27.6 - - + +
142P LEU* 4.5 12.9 - - + +
145P GLU* 4.2 13.7 - - - +
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Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K VAL* 2.6 23.7 + - + +
22K LYS* 3.8 9.9 - - - +
24K GLU* 1.3 73.1 - - - +
26K ASP* 1.3 63.9 + - - +
28K VAL* 3.5 18.2 + - + +
126P LYS* 4.9 12.7 + - - +
131P HIS* 4.3 14.8 - - + +
134P GLU* 3.6 37.9 - - + +
135P LEU* 3.5 28.5 - - + +
138P SER* 3.0 23.1 + - - +
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Residues in contact with ASP 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K LYS 2.9 20.4 - - - +
23K LYS* 3.5 16.6 - - - +
24K GLU 3.1 0.6 - - - -
25K LEU* 1.3 82.0 - - - +
27K LEU* 1.3 65.0 + - + +
28K VAL 3.3 5.1 + - - +
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Residues in contact with LEU 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LYS 3.4 15.9 - - - +
24K GLU* 3.0 32.3 + - - +
26K ASP* 1.3 80.0 - - + +
28K VAL* 1.3 64.4 + - - +
29K PRO* 3.0 12.0 - - - +
141P LYS* 5.7 1.4 + - - -
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Residues in contact with VAL 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K GLU 3.6 3.6 + - - +
25K LEU* 3.5 20.9 - - + +
26K ASP 3.3 6.5 - - - +
27K LEU* 1.3 76.3 - - - +
29K PRO* 1.3 74.0 - - + +
30K THR* 3.7 10.4 + - - +
36K LEU* 4.1 8.1 - - + -
134P GLU* 4.3 23.3 - - + +
137P LEU* 4.5 18.6 - - + -
138P SER* 3.5 22.9 - - - +
141P LYS* 5.8 5.4 - - + +
185P VAL* 5.3 0.2 - - + -
189P ARG* 3.7 23.6 - - - +
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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