Contacts of the helix formed by residues 23 - 32 (chain B) in PDB entry 2P1Q
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 LEU 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LYS* 5.9 4.7 - - - +
21B ILE 3.8 0.2 - - - -
22B GLN* 1.3 82.1 - - + +
24B ASP* 1.3 66.6 + - - +
25B LYS* 4.4 7.0 - - + +
26B ASP* 3.0 42.4 + - - +
27B ARG* 3.0 12.5 + - - +
47B LYS* 4.7 1.3 - - - +
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Residues in contact with ASP 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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159A PHE 3.7 21.1 - - - +
160A GLU* 4.5 8.1 - - + +
22B GLN 3.6 1.1 + - - +
23B LEU* 1.3 70.7 - - - +
25B LYS* 1.3 59.0 + - + +
27B ARG* 3.2 10.5 + - - +
28B ASN* 2.9 35.5 + - - -
45B ARG* 4.5 4.8 + - - +
47B LYS* 3.3 37.3 + - - +
48B VAL* 5.1 0.2 - - - -
49B PHE* 3.3 33.6 + - - +
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Residues in contact with LYS 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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160A GLU* 3.7 44.5 + - + +
23B LEU* 3.2 8.0 - - + +
24B ASP* 1.3 78.6 - - + +
26B ASP* 1.3 63.4 + - - +
28B ASN* 3.6 2.4 + - - +
29B SER* 3.1 27.2 + - - -
484B ARG* 6.3 1.6 - - - +
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Residues in contact with ASP 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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125A ILE* 4.8 2.7 - - + +
126A LYS* 3.8 24.8 + - - +
127A GLY* 3.0 29.7 + - - -
128A LYS 4.6 2.3 + - - +
21B ILE* 3.4 23.5 - - + +
22B GLN 5.7 0.2 + - - -
23B LEU* 3.0 33.2 + - + +
25B LYS* 1.3 79.0 - - - +
27B ARG* 1.3 64.2 + - - +
29B SER* 3.3 6.2 + - - +
30B VAL* 3.0 28.5 + - + +
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Residues in contact with ARG 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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18B PHE* 2.4 41.5 + - - +
19B SER* 4.2 0.8 - - - +
21B ILE* 2.9 22.3 + - - +
22B GLN* 3.5 19.2 + - - +
23B LEU 3.0 17.4 + - - +
24B ASP* 3.4 11.2 - - - +
26B ASP* 1.3 75.1 - - - +
28B ASN* 1.3 56.8 + - - +
30B VAL* 3.4 8.5 + - - +
31B SER* 3.0 25.6 + - - -
41B GLU* 2.8 42.6 + - - +
44B CYS* 3.3 40.6 + - - -
45B ARG* 3.5 35.1 - - + +
46B ARG* 5.8 0.2 - - - +
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Residues in contact with ASN 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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155A ASN* 3.0 49.9 + - + +
159A PHE* 3.6 9.5 + - - +
160A GLU* 2.6 37.2 + - - +
24B ASP 2.9 17.6 + - - +
25B LYS 3.7 3.1 - - - +
26B ASP 3.2 0.2 - - - -
27B ARG* 1.3 73.0 - - - +
29B SER* 1.3 64.4 + - - +
31B SER* 2.6 20.4 + - - -
32B LEU* 3.4 6.8 + - - +
45B ARG* 2.9 28.6 + - - -
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Residues in contact with SER 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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128A LYS 3.3 26.0 + - - -
129A THR* 4.6 0.9 - - - -
130A PRO* 3.6 27.5 - - - +
133A ILE* 4.2 5.8 - - - -
25B LYS 3.1 18.6 + - - -
26B ASP* 3.3 7.3 + - - -
28B ASN* 1.3 74.8 - - - +
30B VAL* 1.3 65.0 + - - +
32B LEU* 3.0 13.8 + - - -
33B VAL* 3.4 12.5 + - - +
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Residues in contact with VAL 30 (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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125A ILE* 3.4 31.9 - - + -
133A ILE* 4.6 0.4 - - - +
18B PHE* 3.5 37.0 - - + -
21B ILE* 4.4 12.8 - - + -
26B ASP 3.0 19.5 + - - +
27B ARG* 3.4 10.3 - - - +
29B SER* 1.3 75.2 - - - +
31B SER* 1.3 63.6 + - - +
32B LEU 3.0 1.7 + - - -
33B VAL* 3.1 22.1 + - - +
37B TRP* 3.4 13.6 - - + +
41B GLU* 3.7 19.7 - - + -
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Residues in contact with SER 31 (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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143A PHE* 3.7 6.6 - - - -
151A VAL* 4.2 2.1 - - - +
155A ASN* 2.9 17.3 + - - -
27B ARG 3.0 8.1 + - - -
28B ASN* 2.6 21.9 + - - -
30B VAL* 1.3 77.5 - - - +
32B LEU* 1.3 56.7 + - - +
33B VAL 3.6 0.4 - - - -
38B TYR* 3.3 43.8 + - - +
41B GLU* 3.6 17.5 - - - -
64B ARG* 3.4 22.5 + - - -
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Residues in contact with LEU 32 (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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130A PRO* 3.6 15.7 - - + +
134A ARG* 3.1 13.5 + - - -
143A PHE* 3.6 15.2 - - + -
148A GLU* 3.8 38.8 - - + +
151A VAL* 3.5 29.8 - - + -
152A ARG* 3.9 36.3 - - + +
155A ASN* 3.8 15.9 - - + +
28B ASN 3.9 6.7 - - - +
29B SER* 3.0 9.8 + - - +
30B VAL 3.0 1.6 + - - -
31B SER* 1.3 78.7 + - - +
33B VAL* 1.3 63.4 + - - +
34B CYS 3.5 0.9 - - - -
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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