Contacts of the helix formed by residues 18 - 23 (chain G) in PDB entry 5B32
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 18 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ALA* 4.4 0.8 - - - +
17G VAL* 1.3 72.4 - - - +
19G ARG* 1.3 63.6 + - - +
20G SER* 3.7 8.0 + - - -
21G GLN* 2.7 48.8 + - - +
22G ARG* 3.2 15.8 + - - +
119I T 5.8 0.9 - - - -
120I T 5.1 14.1 - - - -
176J A 5.4 0.2 - - - -
177J G 3.7 19.7 - - - -
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Residues in contact with ARG 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G VAL 5.3 1.3 - - - +
18G SER* 1.3 71.3 - - - +
20G SER* 1.3 64.3 + - - +
22G ARG* 3.6 13.4 + - - +
23G ALA* 3.3 22.9 + - - +
29G VAL* 3.8 32.9 - - + +
30G GLY* 4.0 10.1 - - - -
33G HIS* 3.1 48.2 + - - +
48G ALA* 3.6 23.6 + - - +
121H TYR* 3.2 34.8 + - + -
177J G 2.9 35.9 + - - +
178J T 5.6 4.5 - - - +
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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
----------------------------------------------------------
18G SER* 3.2 7.3 + - - -
19G ARG* 1.3 77.2 - - - +
21G GLN* 1.3 61.7 + - - +
23G ALA 3.4 1.7 + - - -
24G GLY 3.1 3.3 + - - -
25G LEU* 2.8 41.6 + - - +
26G GLN 4.9 2.7 - - - -
27G PHE 2.7 29.0 + - - -
28G PRO* 3.3 5.2 - - - +
29G VAL* 2.9 25.6 + - - +
177J G 4.7 0.8 + - - -
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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
----------------------------------------------------------
16G ALA* 4.8 4.4 - - - +
17G VAL* 3.3 20.4 - - + +
18G SER* 2.7 47.9 + - - +
20G SER* 1.3 81.1 - - - +
22G ARG* 1.3 58.0 + - - +
24G GLY* 3.0 19.4 + - - -
25G LEU 4.8 2.9 - - - +
120H LYS* 5.1 2.8 - - - -
120I T 4.9 9.2 + - - -
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Residues in contact with ARG 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G VAL* 4.2 27.1 - - + -
18G SER 3.2 16.5 + - - +
19G ARG* 4.0 14.9 - - - +
20G SER 3.4 0.2 - - - -
21G GLN* 1.3 75.7 - - - +
23G ALA* 1.3 56.4 + - - +
24G GLY 3.3 0.4 - - - -
120H LYS* 3.1 32.3 - - - +
121H TYR* 2.8 67.9 + - + -
122H THR* 5.0 0.6 - - - +
124H ALA* 3.2 35.8 + - + +
178J T 5.6 4.2 + - - -
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Residues in contact with ALA 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG 3.3 15.4 + - - +
20G SER* 4.0 4.0 - - - +
21G GLN 3.1 0.8 - - - -
22G ARG* 1.3 77.3 - - - +
24G GLY* 1.3 63.0 + - - +
25G LEU* 3.7 18.5 - - + +
29G VAL* 4.9 0.4 - - + -
52G VAL* 3.7 20.9 - - + -
117H ALA* 3.7 34.2 - - - +
120H LYS* 4.1 9.4 - - - +
121H TYR* 4.0 6.3 - - + +
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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
------------------------------------------------------------
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