Contacts of the helix formed by residues 15 - 24 (chain G) in PDB entry 1RZR
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 15 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ALA* 4.8 0.2 - - - -
14G VAL* 1.3 75.1 - - - +
16G MSE 1.3 54.8 + - - +
17G ALA* 2.7 7.1 + - - -
18G THR* 2.5 36.2 + - - -
19G VAL* 3.1 11.0 + - - +
702H G 2.3 75.5 + - - -
703H A 5.1 1.8 - - - -
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Residues in contact with MSE 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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5G ILE* 3.4 32.9 - - + +
6G TYR* 3.8 40.2 - - + +
9G ALA* 4.0 8.6 - - + +
14G VAL 4.1 1.2 + - - -
15G SER* 1.3 71.2 - - - +
17G ALA* 1.3 56.4 + - - +
19G VAL* 3.5 12.6 + - - +
20G SER* 3.0 27.2 + - - -
704H A 5.9 2.9 - - - +
709R C 3.6 20.0 - - + +
710R T 3.5 30.7 - - + +
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Residues in contact with ALA 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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15G SER* 2.7 2.5 + - - +
16G MSE 1.3 76.7 - - - +
18G THR* 1.3 60.0 + - - +
20G SER* 3.5 2.8 - - - -
21G ARG* 3.0 39.8 + - - +
702H G 3.9 20.0 - - + +
703H A 3.0 37.1 + - + +
704H A 5.1 0.4 - - - +
711R T 3.3 16.7 + - + +
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Residues in contact with THR 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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14G VAL* 3.7 13.2 - - + -
15G SER* 2.5 21.4 + - - -
17G ALA* 1.3 70.3 - - - +
19G VAL* 1.3 65.7 + - - +
21G ARG* 3.1 16.2 + - - +
22G VAL* 3.1 18.4 + - - +
29G VAL* 4.6 17.9 - - + -
33G THR* 3.8 28.5 - - + -
37G VAL* 4.0 7.2 - - + -
701H T 3.8 15.8 - - + +
702H G 2.5 29.0 + - - +
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Residues in contact with VAL 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ILE* 3.6 29.6 - - + +
8G VAL* 3.8 31.6 - - + -
9G ALA* 4.1 10.3 - - - +
14G VAL* 3.7 17.9 - - + -
15G SER 3.1 12.5 + - - +
16G MSE 3.7 12.8 - - - +
18G THR* 1.3 76.7 - - - +
20G SER* 1.3 62.3 + - - +
22G VAL* 3.2 5.5 - - - +
23G VAL* 3.0 29.6 + - + +
37G VAL* 4.1 13.5 - - + -
41G ILE* 4.4 5.4 - - + -
46G TYR* 5.7 0.9 - - + -
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Residues in contact with SER 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ILE* 4.5 4.7 - - - -
16G MSE 3.0 18.6 + - - -
17G ALA 3.5 6.3 - - - -
19G VAL* 1.3 78.4 - - - +
21G ARG* 1.3 59.0 + - - +
23G VAL* 3.3 2.7 + - - +
24G ASN* 3.0 42.5 + - - -
710R T 3.3 34.3 + - - -
711R T 3.2 26.2 - - - +
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Residues in contact with ARG 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 ALA* 3.0 22.4 + - - +
18G THR* 3.1 4.6 + - - +
20G SER* 1.3 81.6 - - - +
22G VAL* 1.3 57.8 + - - +
24G ASN* 3.7 4.7 - - - +
25G GLY* 2.9 3.6 + - - -
26G ASN* 2.9 49.6 + - + +
27G PRO 5.6 3.6 - - - -
28G ASN 5.6 0.2 - - - -
29G VAL* 4.3 20.1 - - + +
34G ARG* 4.7 1.0 + - - -
701H T 2.9 58.5 + - - +
702H G 3.4 31.3 + - - -
703H A 5.1 1.2 - - - +
711R T 4.5 9.9 - - + +
712R T 4.0 19.6 + - - +
713R C 4.1 0.6 - - - +
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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 THR 3.1 13.0 + - - +
19G VAL 3.2 10.8 - - - +
21G ARG* 1.3 74.1 - - - +
23G VAL* 1.3 74.1 + - - +
24G ASN 3.0 1.6 - - - -
25G GLY* 2.5 24.3 + - - +
29G VAL* 4.3 11.9 - - + -
34G ARG* 4.1 38.0 + - + +
37G VAL* 3.3 39.3 - - + -
38G LEU* 4.7 12.7 - - + +
41G ILE* 3.8 12.3 - - + -
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Residues in contact with VAL 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ILE* 5.1 3.1 - - + -
19G VAL* 3.0 20.5 + - + +
20G SER* 3.8 6.3 - - - +
22G VAL* 1.3 85.0 - - - +
24G ASN* 1.3 65.2 + - - +
25G GLY 3.4 0.2 + - - -
38G LEU* 6.2 1.1 - - - -
41G ILE* 4.2 20.6 - - + -
46G TYR* 4.2 19.1 - - + -
48G PRO* 4.3 25.4 - - + -
53G ARG* 6.5 0.4 - - - -
710R T 5.1 8.3 - - - +
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Residues in contact with ASN 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 SER* 3.0 34.7 + - - +
21G ARG* 4.0 5.9 - - - +
23G VAL* 1.3 79.3 - - - +
25G GLY* 1.3 65.5 + - - +
26G ASN* 3.3 19.8 + - - +
53G ARG* 4.8 5.2 - - - -
710R T 3.3 36.7 + - - +
711R T 5.3 2.4 + - - -
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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