Contacts of the helix formed by residues 17 - 22 (chain G) in PDB entry 6T90
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 THR 17 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ALA* 3.4 4.3 - - + +
16G LYS* 1.3 86.0 - - + +
18G ARG* 1.3 63.0 + - - +
19G SER* 3.9 7.4 + - - -
20G SER* 3.2 26.7 + - - -
21G ARG* 3.3 23.2 + - - +
121I G 4.3 28.0 - - - +
30J G 5.7 0.4 - - - +
31J A 3.9 17.7 - - - +
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Residues in contact with ARG 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G THR* 1.3 72.4 - - - +
19G SER* 1.3 66.6 + - - +
21G ARG* 3.3 16.4 + - - +
22G ALA* 3.1 24.6 + - - +
28G VAL* 3.9 29.9 - - + +
29G GLY* 4.5 3.8 - - - -
32G HIS* 4.4 24.2 + - - +
46G ALA* 3.5 27.3 + - - +
49G PRO* 4.0 10.9 - - - +
50G VAL* 4.6 0.4 - - - +
122H TYR* 2.8 38.9 + - + +
31J A 3.2 40.0 + - - +
32J G 5.4 1.6 - - - +
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Residues in contact with SER 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G THR* 3.3 7.5 + - - -
18G ARG* 1.3 78.3 - - - +
20G SER* 1.3 62.2 + - - +
22G ALA* 3.4 1.4 + - - -
23G GLY 3.1 3.3 + - - -
24G LEU* 2.8 39.9 + - - -
25G GLN 5.0 2.5 - - - -
26G PHE 2.7 27.7 + - - -
27G PRO* 3.3 5.4 - - - +
28G VAL* 3.2 24.6 + - - -
31J A 4.7 1.1 + - - -
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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
----------------------------------------------------------
13G ALA* 3.3 20.1 - - - +
14G LYS 4.3 2.1 + - - -
15G ALA* 3.3 28.2 - - - +
17G THR* 3.2 20.4 + - - -
18G ARG 3.2 0.4 - - - -
19G SER* 1.3 79.3 - - - +
21G ARG* 1.3 65.1 + - - +
23G GLY* 2.8 16.5 + - - -
24G LEU 4.8 2.5 - - - -
121H LYS* 4.3 0.2 + - - -
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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
----------------------------------------------------------
13G ALA* 3.7 11.0 - - + -
15G ALA 4.6 13.7 + - - +
16G LYS* 3.4 20.7 + - - +
17G THR 3.3 13.8 + - - +
18G ARG* 3.3 17.4 + - - +
20G SER* 1.3 77.8 - - - +
22G ALA* 1.3 62.3 + - - +
23G GLY 3.3 0.2 + - - -
121H LYS* 3.4 26.9 - - - +
122H TYR* 3.8 25.7 + - + -
125H ALA* 3.0 42.3 + - + +
32J G 3.0 32.8 + - - -
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Residues in contact with ALA 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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10G LYS* 5.8 0.9 - - - +
18G ARG 3.1 14.0 + - - +
19G SER 4.0 0.4 - - - +
21G ARG* 1.3 78.1 - - - +
23G GLY* 1.3 60.9 + - - +
24G LEU* 3.5 24.0 + - + +
28G VAL* 4.9 1.8 - - + -
50G VAL* 3.7 30.3 - - + -
118H ALA* 3.9 24.5 - - + +
121H LYS* 4.2 7.4 - - - +
122H TYR* 4.1 6.7 - - + +
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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
------------------------------------------------------------
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