Contacts of the helix formed by residues 20 - 29 (chain B) in PDB entry 3QBK
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 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B GLU 3.6 3.2 + - - -
19B VAL* 1.3 77.1 - - - +
21B GLN* 1.3 63.5 + - - +
22B ARG* 3.1 33.0 - - + +
23B GLU* 3.1 42.6 + - + +
24B LEU* 3.0 20.1 + - - +
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU 3.1 21.6 + - - -
169A THR* 3.2 12.2 - - - +
170A THR* 2.7 40.1 + - - +
171A SER* 3.3 9.2 + - - -
19B VAL 4.2 0.6 + - - -
20B THR* 1.3 73.4 + - - +
22B ARG* 1.3 63.2 + - - +
24B LEU* 3.3 10.2 + - - +
25B PHE* 3.0 22.5 + - - +
87B SER 3.9 3.1 - - - +
88B GLY* 3.4 24.9 - - - +
89B LEU* 3.5 25.4 + - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 5.9 1.6 - - - +
98A ALA* 5.9 7.4 - - - +
170A THR* 4.8 4.7 + - - +
171A SER* 3.5 39.0 - - - +
20B THR* 3.1 16.5 - - + +
21B GLN* 1.3 78.3 - - - +
23B GLU* 1.3 60.3 + - - +
25B PHE* 3.3 5.1 - - + +
26B GLU* 2.8 56.3 + - + +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU 4.8 0.5 - - - +
19B VAL* 3.5 16.6 - - + +
20B THR* 3.1 40.8 + - + +
22B ARG* 1.3 79.2 - - + +
24B LEU* 1.3 55.7 + - - +
26B GLU* 3.2 15.2 + - - +
27B PHE* 2.7 34.4 + - - +
109B LEU* 4.2 21.7 - - + +
112B GLU* 3.7 29.4 - - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.1 26.5 - - + -
20B THR 3.0 30.9 + - - +
21B GLN* 3.3 7.8 + - - +
23B GLU* 1.3 79.4 - - - +
25B PHE* 1.3 57.3 + - - +
27B PHE* 3.2 8.4 + - + +
28B VAL* 2.9 34.7 + - - +
88B GLY* 4.1 14.1 - - - +
91B ILE* 3.9 41.1 - - + +
92B SER* 5.1 10.1 - - - -
93B VAL* 5.2 5.6 - - + -
107B VAL* 6.0 0.2 - - + -
109B LEU* 4.5 12.8 - - + -
118B VAL* 5.2 11.4 - - + -
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A SER* 3.5 29.8 - - - -
172A SER* 3.8 26.0 - - - -
175A MET* 4.2 8.3 - - + -
21B GLN 3.0 13.8 + - - +
22B ARG* 3.3 12.8 - - + +
24B LEU* 1.3 79.0 - - - +
26B GLU* 1.3 72.1 + - + +
28B VAL* 3.4 4.2 + - - +
29B LEU* 3.3 44.5 + - + +
39B TYR* 3.6 19.3 - - - -
86B ALA 3.3 26.0 - - - -
87B SER* 3.6 8.5 - - - +
88B GLY* 4.3 0.6 - - - -
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 2.8 53.6 + - - +
23B GLU* 3.2 17.0 + - - +
25B PHE* 1.3 86.4 - - + +
27B PHE* 1.3 56.2 + - - +
29B LEU* 2.5 33.0 - - + +
30B ASN* 2.9 27.4 + - - +
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 2.7 17.0 + - - +
24B LEU* 3.2 12.5 + - + +
26B GLU* 1.3 73.5 - - - +
28B VAL* 1.3 57.8 + - + +
29B LEU 2.6 18.1 - - - +
30B ASN* 4.5 4.0 - - - +
31B ASP* 3.5 24.4 - - + +
34B LEU* 3.5 27.1 - - + -
91B ILE* 6.5 0.2 - - + -
107B VAL* 3.7 22.2 - - + -
108B MET 3.9 15.0 - - - -
109B LEU* 4.0 17.5 - - + +
118B VAL* 3.6 32.8 - - + -
241B VAL* 4.6 10.5 - - + -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU 2.9 20.0 + - - +
25B PHE 3.6 7.9 - - - +
26B GLU 3.2 0.2 - - - -
27B PHE* 1.3 76.2 - - + +
29B LEU* 1.3 67.0 + - - +
31B ASP* 3.1 21.8 - - - +
34B LEU* 4.1 16.8 - - + -
35B ALA* 3.2 26.9 + - - +
38B LEU* 4.0 17.5 - - + -
39B TYR* 4.1 17.3 - - + -
85B LEU 4.3 8.1 - - - +
86B ALA* 4.4 9.4 - - - +
91B ILE* 4.1 24.5 - - + -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PHE* 3.3 40.8 + - + +
26B GLU* 2.5 22.1 - - + +
27B PHE 2.6 9.7 - - - +
28B VAL* 1.3 80.9 - - - +
30B ASN* 1.3 64.6 + - - +
31B ASP 2.7 4.5 + - - -
35B ALA* 4.2 11.0 - - + -
39B TYR* 3.9 31.9 - - + +
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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