Contacts of the helix formed by residues 13 - 25 (chain K) in PDB entry 5NSS
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 ASN 13 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11K GLU 3.7 2.0 + - - +
12K ALA* 1.3 69.1 - - - +
14K SER* 1.3 59.1 + - - +
15K PHE 3.2 2.9 - - - -
16K LEU* 3.0 15.0 + - + +
17K GLU* 2.9 29.1 + - - +
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Residues in contact with SER 14 (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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12K ALA* 3.2 11.0 - - - +
13K ASN* 1.3 78.9 - - - +
15K PHE* 1.3 56.6 + - - +
17K GLU* 4.1 6.1 - - - +
18K VAL* 2.9 32.7 + - - +
177K PRO* 3.7 32.4 - - - +
178K PRO 5.5 0.4 - - - -
181K GLU* 5.1 6.3 - - - -
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Residues in contact with PHE 15 (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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8K LEU* 5.7 8.7 - - + -
9K LEU 5.4 8.1 - - - +
10K GLY 5.8 2.7 - - - +
12K ALA* 3.7 11.8 + - + +
13K ASN 3.2 0.8 - - - -
14K SER* 1.3 78.4 - - - +
16K LEU* 1.3 51.6 + - - +
18K VAL* 4.8 2.5 - - - -
19K LEU* 2.7 41.4 + - - +
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Residues in contact with LEU 16 (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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12K ALA 4.5 0.8 + - - +
13K ASN* 3.0 18.9 + - + +
15K PHE* 1.3 78.1 - - - +
17K GLU* 1.3 59.8 + - - +
19K LEU* 4.5 2.5 - - - -
20K GLU* 2.9 31.5 + - - +
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Residues in contact with GLU 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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13K ASN 2.9 14.3 + - - +
14K SER* 4.1 6.3 - - - +
16K LEU* 1.3 76.0 - - - +
18K VAL* 1.3 60.0 + - - +
20K GLU* 3.8 3.5 - - - +
21K GLN* 2.9 30.1 + - - +
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Residues in contact with VAL 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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14K SER 2.9 18.7 + - - +
15K PHE* 4.6 2.9 - - - +
17K GLU* 1.3 77.0 - - - +
19K LEU* 1.3 59.1 + - - +
21K GLN* 3.8 4.9 - - - +
22K VAL* 2.9 30.5 + - - +
175K GLN 5.5 6.1 - - - +
177K PRO* 6.5 0.7 - - + -
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Residues in contact with LEU 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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15K PHE 2.7 24.0 + - - +
16K LEU* 4.3 3.1 - - - +
18K VAL* 1.3 76.4 - - - +
20K GLU* 1.3 58.9 + - - +
22K VAL* 3.9 5.0 - - - +
23K SER* 2.9 31.2 + - - -
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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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16K LEU 2.9 23.9 + - - +
17K GLU* 3.9 4.3 - - - +
19K LEU* 1.3 77.3 - - - +
21K GLN* 1.3 57.0 + - - +
23K SER* 3.9 3.9 - - - -
24K HIS* 2.9 31.5 + - - +
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Residues in contact with GLN 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 GLU 2.9 18.8 + - - +
18K VAL* 3.9 5.8 - - - +
20K GLU* 1.3 76.9 - - - +
22K VAL* 1.3 62.4 + - - +
24K HIS* 4.1 4.9 - - - +
25K LEU* 3.3 24.1 + - - +
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Residues in contact with VAL 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 VAL 2.9 18.2 + - - +
19K LEU* 3.9 5.8 - - - +
21K GLN* 1.3 76.5 - - - +
23K SER* 1.3 64.2 + - - +
25K LEU* 3.4 5.7 + - - +
26K ALA* 3.3 19.4 + - - +
49K LEU* 4.4 27.7 - - + +
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Residues in contact with SER 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 LEU 2.9 19.6 + - - -
20K GLU* 4.2 4.3 - - - -
22K VAL* 1.3 73.9 - - - +
24K HIS* 1.3 64.1 + - - +
26K ALA* 3.4 20.2 + - - +
27K PRO 4.7 0.9 - - - -
52K LEU* 5.0 12.3 - - - +
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Residues in contact with HIS 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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238J TYR* 5.1 23.3 - - + +
239J ARG* 5.9 2.7 - - - -
20K GLU 2.9 21.2 + - - +
21K GLN* 4.1 6.1 - - - +
22K VAL 3.3 0.2 - - - -
23K SER* 1.3 77.4 - - - +
25K LEU* 1.3 58.0 + - - +
26K ALA 3.3 1.0 + - - -
27K PRO* 4.4 8.1 - - - +
28K LEU* 5.2 0.7 + - - +
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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 GLN 3.3 18.9 + - - +
22K VAL* 3.8 5.6 - - - +
23K SER 3.3 0.4 - - - -
24K HIS* 1.3 74.3 - - - +
26K ALA* 1.3 63.9 + - - +
27K PRO 3.4 2.0 - - - -
28K LEU* 3.3 28.5 + - + +
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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