Contacts of the helix formed by residues 19 - 29 (chain B) in PDB entry 2QXU
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 PHE 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B MET* 3.6 42.8 - - + -
9B VAL 3.5 27.1 - - - -
10B HIS* 3.5 28.7 - - + -
15B ALA 4.4 3.6 - - - -
16B SER* 3.7 15.9 - - - +
17B PHE 2.9 1.4 - - - -
18B ASN* 1.3 80.9 - - + +
20B ALA* 1.3 63.5 + - - +
21B GLY 3.2 2.7 - - - -
22B ILE* 3.4 27.2 + - + +
23B LYS* 3.0 28.6 + - - +
38B ALA* 4.3 6.1 - - + -
74B VAL* 3.9 14.8 - - + -
76B HIS* 4.1 14.4 - - + -
102B LEU* 4.7 0.4 - - + -
160B LEU* 3.8 15.5 - - + -
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Residues in contact with ALA 20 (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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16B SER 4.6 0.2 + - - -
17B PHE* 3.1 19.6 + - + +
18B ASN 3.4 1.6 - - - -
19B PHE* 1.3 77.1 - - - +
21B GLY* 1.3 62.5 + - - +
23B LYS* 3.5 7.2 + - - +
24B SER* 3.2 26.3 + - - -
33B ARG* 5.1 0.2 + - - -
161B TYR* 5.3 4.5 - - + +
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Residues in contact with GLY 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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19B PHE 3.2 0.4 - - - -
20B ALA* 1.3 77.3 - - - +
22B ILE* 1.3 64.5 + - - +
24B SER* 3.2 6.9 + - - -
25B TYR* 3.0 23.7 + - - +
160B LEU 4.5 1.8 - - - -
161B TYR* 4.1 26.0 - - - -
166B ASN* 5.1 2.4 + - - -
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Residues in contact with ILE 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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8B MET* 4.5 9.4 - - + -
19B PHE* 3.4 33.2 + - + +
21B GLY* 1.3 74.2 - - - +
23B LYS* 1.3 62.6 + - - +
25B TYR* 3.3 7.5 + - + +
26B LEU* 3.0 44.5 + - + +
74B VAL* 4.5 5.6 - - + -
102B LEU* 3.8 26.5 - - + -
159B LEU 4.8 0.4 - - - +
160B LEU* 3.7 27.2 + - + +
166B ASN* 4.0 9.2 - - - +
169B ILE* 3.8 27.6 - - + -
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Residues in contact with LYS 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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8B MET* 4.0 19.7 - - - +
16B SER 5.3 2.8 + - - -
19B PHE* 3.0 18.6 + - - +
20B ALA* 3.6 7.6 - - - +
22B ILE* 1.3 79.2 - - - +
24B SER* 1.3 61.3 + - - +
26B LEU 3.3 0.3 + - - -
27B VAL* 3.0 27.9 + - - +
33B ARG* 3.7 26.2 - - - +
36B LEU* 3.6 51.8 + - + +
38B ALA* 4.1 22.8 - - - +
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Residues in contact with SER 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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20B ALA 3.2 12.0 + - - -
21B GLY* 3.7 8.3 - - - -
23B LYS* 1.3 79.4 - - - +
25B TYR* 1.3 61.6 + - - +
27B VAL* 3.5 2.8 + - - +
28B SER* 3.1 22.5 + - - -
33B ARG* 3.6 25.7 + - - +
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Residues in contact with TYR 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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21B GLY 3.0 13.2 + - - +
22B ILE* 3.5 9.2 - - + +
23B LYS 3.2 0.2 - - - -
24B SER* 1.3 74.7 - - - +
26B LEU* 1.3 82.2 + - + +
28B SER* 2.5 28.2 + - - -
29B GLN* 3.1 35.6 + - + +
163B SER 5.6 0.2 - - - -
166B ASN* 3.1 65.7 + - + +
167B SER* 3.7 12.4 + - - -
169B ILE* 5.5 1.1 - - + -
170B LYS* 3.6 27.9 - - + +
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Residues in contact with LEU 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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6B VAL* 4.9 0.2 - - + -
8B MET* 3.8 26.7 - - + -
22B ILE* 3.0 30.8 + - + +
23B LYS 3.8 3.4 - - - +
25B TYR* 1.3 91.2 - - + +
27B VAL* 1.3 56.3 + - - +
29B GLN* 2.7 24.0 + - - +
30B GLY 3.1 9.2 + - - -
31B TRP* 3.1 41.5 + - + +
36B LEU* 4.0 12.3 - - + -
74B VAL* 5.4 0.4 - - + -
169B ILE* 4.3 7.2 - - + -
170B LYS* 4.9 2.0 - - - -
173B LEU* 3.8 33.4 - - + -
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Residues in contact with VAL 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 LYS 3.0 18.8 + - - +
24B SER 3.7 5.6 - - - +
26B LEU* 1.3 74.3 - - - +
28B SER* 1.3 62.6 + - - +
29B GLN 3.1 1.2 + - - -
30B GLY* 3.2 10.9 + - - -
31B TRP 3.4 16.2 - - - +
33B ARG* 3.4 53.6 - - + +
36B LEU* 3.8 16.6 - - + -
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Residues in contact with SER 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 SER 3.1 12.7 + - - -
25B TYR* 2.5 27.8 + - - -
27B VAL* 1.3 77.1 - - - +
29B GLN* 1.3 75.4 + - - +
30B GLY 3.5 0.8 + - - -
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Residues in contact with GLN 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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3B HIS* 4.9 2.4 - - - -
25B TYR* 3.4 46.8 + - + +
26B LEU* 2.7 11.3 + - - +
28B SER* 1.3 101.0 + - - +
30B GLY* 1.3 55.8 + - - +
31B TRP* 3.7 25.6 - - + -
170B LYS* 3.0 35.2 + - + +
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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