Contacts of the helix formed by residues 12 - 25 (chain G) 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 ALA 12 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G GLY* 3.4 3.1 - - - +
11G GLU* 1.3 82.7 - - - +
13G ASN* 1.3 64.6 + - - +
14G SER* 3.2 8.7 - - - +
15G PHE* 3.2 19.5 + - + +
16G LEU* 3.5 6.8 + - - +
177G PRO* 4.6 15.9 - - + -
181G GLU* 3.7 39.2 + - + +
182G ARG* 4.9 0.9 - - - +
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Residues in contact with ASN 13 (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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11G GLU 3.9 0.4 + - - -
12G ALA* 1.3 74.5 - - - +
14G SER* 1.3 58.5 + - - +
16G LEU* 3.2 6.8 + - - +
17G GLU* 2.9 31.3 + - - +
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Residues in contact with SER 14 (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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12G ALA* 3.2 7.4 - - - +
13G ASN* 1.3 78.3 - - - +
15G PHE* 1.3 58.9 + - - +
16G LEU 3.4 0.2 - - - -
17G GLU* 4.5 5.6 - - - +
18G VAL* 2.9 35.0 + - - +
175G GLN* 4.8 14.9 - - - +
176G LEU 5.8 0.2 - - - -
177G PRO* 5.1 11.2 - - - -
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Residues in contact with PHE 15 (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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8G LEU* 3.9 14.1 - - + +
9G LEU 3.2 27.8 - - - +
10G GLY* 3.6 15.0 - - - +
12G ALA* 3.2 14.7 + - - +
13G ASN 3.2 0.8 - - - -
14G SER* 1.3 79.4 - - - +
16G LEU* 1.3 50.7 + - - +
18G VAL* 4.8 0.4 - - - -
19G LEU* 2.6 39.0 + - - +
177G PRO* 4.7 11.7 - - + +
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Residues in contact with LEU 16 (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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12G ALA 3.5 7.1 + - - +
13G ASN* 3.2 9.2 + - - +
15G PHE* 1.3 77.5 - - - +
17G GLU* 1.3 60.2 + - - +
19G LEU* 3.7 3.9 - - - +
20G GLU* 2.9 31.0 + - - +
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Residues in contact with GLU 17 (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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13G ASN 2.9 16.6 + - - +
14G SER* 4.4 4.9 - - - +
16G LEU* 1.3 77.8 - - - +
18G VAL* 1.3 57.9 + - - +
20G GLU* 4.0 3.3 - - - +
21G GLN* 2.9 33.2 + - - +
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Residues in contact with VAL 18 (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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8G LEU* 5.2 6.7 - - + +
14G SER* 2.9 21.5 + - - +
15G PHE* 4.6 1.6 - - - +
17G GLU* 1.3 76.9 - - - +
19G LEU* 1.3 53.3 + - - +
20G GLU 3.4 0.2 - - - -
21G GLN* 4.7 3.1 - - - -
22G VAL* 2.7 39.6 + - + +
174G VAL* 4.8 15.7 - - + -
175G GLN 4.7 13.2 - - - +
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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
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8G LEU* 4.1 26.7 - - + +
15G PHE 2.6 24.7 + - - +
16G LEU* 3.7 6.1 - - - +
17G GLU 3.2 0.4 - - - -
18G VAL* 1.3 79.0 - - - +
20G GLU* 1.3 50.5 + - - +
22G VAL* 4.6 1.1 - - - +
23G SER* 2.6 39.6 + - - +
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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
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16G LEU 2.9 17.6 + - - +
17G GLU* 4.1 3.6 - - - +
19G LEU* 1.3 75.4 - - - +
21G GLN* 1.3 60.6 + - - +
23G SER* 3.8 3.7 - - - -
24G HIS* 2.9 30.8 + - - +
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Residues in contact with GLN 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 GLU 2.9 19.0 + - - +
18G VAL* 4.6 2.7 - - - +
20G GLU* 1.3 76.8 - - - +
22G VAL* 1.3 58.1 + - - +
24G HIS* 4.0 4.3 - - - +
25G LEU* 3.1 28.8 + - - +
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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
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18G VAL* 2.7 24.8 + - + +
19G LEU* 4.6 0.9 - - - +
21G GLN* 1.3 75.7 - - - +
23G SER* 1.3 60.5 + - - +
25G LEU* 3.5 4.9 - - - +
26G ALA* 2.9 29.3 + - - +
45G ILE* 5.5 10.3 - - + +
49G LEU* 4.3 14.9 - - + +
174G VAL* 5.5 9.6 - - + -
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Residues in contact with SER 23 (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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19G LEU 2.6 24.0 + - - -
20G GLU* 3.8 5.6 - - - -
21G GLN 3.3 0.2 - - - -
22G VAL* 1.3 75.4 - - - +
24G HIS* 1.3 63.9 + - - +
26G ALA* 3.3 19.1 + - - +
27G PRO 4.7 1.0 - - - -
52G LEU* 5.5 1.5 - - - +
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Residues in contact with HIS 24 (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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20G GLU 2.9 19.3 + - - +
21G GLN* 4.1 4.5 - - - +
22G VAL 3.4 0.2 - - - -
23G SER* 1.3 76.3 - - - +
25G LEU* 1.3 59.4 + - - +
26G ALA 3.7 0.5 + - - -
27G PRO* 4.6 6.8 - - - +
28G LEU 5.3 0.3 + - - -
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Residues in contact with LEU 25 (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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21G GLN 3.1 19.7 + - - +
22G VAL* 3.5 5.6 - - - +
24G HIS* 1.3 75.0 - - - +
26G ALA* 1.3 63.2 + - - +
27G PRO 3.4 2.0 - - - -
28G LEU* 3.3 27.3 + - + +
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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