Contacts of the helix formed by residues 25 - 35 (chain K) in PDB entry 4GUN
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 SER 25 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17K LEU 4.3 1.1 - - - -
21K GLU* 3.9 11.2 - - - -
22K PRO 6.2 0.2 - - - -
24K ILE* 1.3 78.0 - - - +
26K LYS* 1.4 63.7 + - - +
27K GLU* 3.2 34.8 - - - +
28K ILE* 3.2 20.9 + - - +
29K ASN* 3.1 22.5 + - - -
178K LEU* 5.4 0.2 - - - +
179K GLN* 3.0 21.5 + - - +
22P PRO* 5.3 7.0 - - - -
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Residues in contact with LYS 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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17K LEU* 3.3 47.9 + - + +
18K ASP* 3.8 19.1 - - + +
21K GLU* 3.1 21.9 + - - +
24K ILE 4.0 0.2 + - - -
25K SER* 1.4 71.4 - - - +
27K GLU* 1.3 59.9 + - - +
29K ASN* 3.3 1.0 + - - +
30K ASP* 2.8 42.1 + - + +
183P VAL* 5.1 2.4 - - - +
186P ASP* 2.9 44.5 + - + +
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Residues in contact with GLU 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K GLU* 4.3 3.8 - - - +
25K SER* 3.2 25.9 - - - +
26K LYS* 1.3 84.7 + - - +
28K ILE* 1.3 61.6 + - - +
30K ASP* 3.8 4.7 + - - +
31K LEU* 3.4 29.6 + - + +
178K LEU* 4.6 16.4 - - + -
22P PRO 4.4 1.4 - - - +
179P GLN* 3.1 45.4 + - + +
180P TYR* 3.9 22.0 + - - -
186P ASP* 5.4 2.1 - - - +
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Residues in contact with ILE 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 ILE* 3.7 14.4 - - + -
25K SER* 3.2 19.8 + - - +
27K GLU* 1.3 74.6 - - - +
29K ASN* 1.4 55.2 + - - +
31K LEU* 3.1 6.6 + - - +
32K HIS* 2.6 43.6 + - + +
174K HIS 4.0 12.1 - - - +
175K ALA* 3.5 24.7 - - - +
176K TYR* 3.8 20.4 - - - +
178K LEU* 4.0 22.0 - - + +
179K GLN* 3.7 40.2 - - + +
180K TYR* 5.3 1.3 - - + -
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Residues in contact with ASN 29 (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 TRP* 3.6 27.8 - - + -
17K LEU* 3.0 39.6 + - + +
20K LEU* 3.8 20.9 - - - +
24K ILE* 3.3 21.0 + - - +
25K SER 3.1 13.2 + - - +
26K LYS 3.8 0.9 - - - +
28K ILE* 1.4 77.8 - - - +
30K ASP* 1.4 57.2 + - - +
32K HIS* 4.0 6.9 + - - -
33K ILE* 3.0 38.9 + - + +
83K PHE* 6.1 0.5 - - - -
84K TRP* 4.8 7.1 - - - -
87K LEU* 5.5 0.7 - - - +
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Residues in contact with ASP 30 (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 LEU* 3.9 24.3 - - + +
26K LYS* 2.8 29.3 + - + +
27K GLU* 4.1 5.4 - - - +
29K ASN* 1.4 71.4 - - - +
31K LEU* 1.3 60.2 + - + +
34K ASN* 2.9 53.9 + - - +
35K LYS* 4.9 0.3 - - - +
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Residues in contact with LEU 31 (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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177I TYR* 3.8 21.3 - - - +
181I GLN* 3.8 28.9 - - + +
182I ASN* 3.5 24.2 - - - +
27K GLU* 3.4 10.0 + - + +
28K ILE* 3.1 7.0 + - - +
30K ASP* 1.3 80.4 - - + +
32K HIS* 1.3 59.7 + - - +
35K LYS* 2.8 44.0 + - + +
36K HIS* 3.1 11.2 + - + -
178K LEU* 3.4 32.8 - - + -
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Residues in contact with HIS 32 (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 ILE* 6.0 0.2 - - - +
28K ILE* 2.6 32.2 + - + +
29K ASN* 3.8 8.9 + - - +
31K LEU* 1.3 72.7 - - - +
33K ILE* 1.3 57.1 + - - +
36K HIS* 3.3 13.1 - - + +
37K HIS* 3.0 26.0 + - - +
80K HIS* 3.2 6.7 + + - -
83K PHE* 3.9 15.7 - + - -
84K TRP* 3.4 26.5 - + + -
170K ASP* 3.1 15.3 - - - -
174K HIS* 3.1 18.0 + + - +
175K ALA* 3.9 18.3 + - + -
301K MN 2.2 31.2 + - - -
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Residues in contact with ILE 33 (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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10K LEU* 3.6 15.3 - - + +
13K ILE* 3.4 35.7 - - + -
15K TRP* 4.0 27.4 - - + -
17K LEU* 3.8 18.8 - - + -
29K ASN* 3.0 19.9 + - + +
32K HIS* 1.3 76.5 - - - +
34K ASN* 1.3 72.9 + - - +
37K HIS* 3.4 6.2 - - - +
38K VAL* 3.4 27.4 + - - +
84K TRP* 3.6 30.7 - - + +
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Residues in contact with ASN 34 (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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10K LEU* 3.9 18.2 - - - +
17K LEU* 4.4 12.1 - - - +
30K ASP* 2.9 42.1 + - - +
33K ILE* 1.3 83.1 - - - +
35K LYS* 1.3 71.7 + - + +
38K VAL* 3.3 23.0 - - + +
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Residues in contact with LYS 35 (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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182I ASN* 3.4 42.0 - - + +
30K ASP 4.9 0.7 - - - +
31K LEU* 2.8 37.2 + - + +
34K ASN* 1.3 84.6 - - + +
36K HIS* 1.4 58.7 + - - +
37K HIS 3.6 0.4 - - - -
38K VAL* 3.6 2.8 + - - +
39K ALA* 3.0 30.2 + - - +
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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
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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