Contacts of the helix formed by residues 17 - 29 (chain B) in PDB entry 3O2Q
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 ASN 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLN* 1.3 81.1 - - + +
18B ARG* 1.3 67.1 + - - +
19B SER 3.4 0.9 - - - -
20B MET* 4.0 0.4 - - - +
21B GLU* 3.0 29.1 + - - +
84B MET* 3.9 11.2 - - - +
87B ARG* 4.1 3.8 + - - +
143B ASP* 3.0 27.8 - - - +
144B ASN* 3.3 24.6 + - - +
145B HIS* 3.6 24.2 - - - +
148B ALA* 3.1 20.2 - - - +
195B PO4 3.1 9.6 + - - +
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Residues in contact with ARG 18 (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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12B SER* 4.2 2.2 - - - +
13B SER* 3.8 12.7 - - - +
17B ASN* 1.3 76.7 - - - +
19B SER* 1.3 61.0 + - - +
21B GLU* 3.7 2.6 + - - +
22B ALA* 3.3 22.5 + - - +
111B CYS* 3.6 37.9 + - + +
112B GLU* 3.0 32.7 + - - +
141B ILE* 2.8 59.6 + - + +
142B GLN* 3.6 12.8 - - - +
143B ASP* 3.9 21.9 + - - +
148B ALA* 4.0 17.7 - - + +
152B ALA* 5.6 0.2 - - - -
155B ILE* 5.8 0.2 - - - +
195B PO4 2.7 45.8 + - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.6 35.8 - - - +
12B SER* 2.6 33.5 + - - -
15B ASN* 3.0 28.7 + - - -
18B ARG* 1.3 77.2 - - - +
20B MET* 1.3 54.2 + - - +
22B ALA* 3.4 1.9 + - - +
23B HIS* 2.7 34.2 + - - +
35B SER* 4.0 4.0 - - - -
36B PHE 3.6 2.5 + - - -
111B CYS* 4.8 0.2 - - - -
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Residues in contact with MET 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN* 3.5 28.0 - - - +
16B GLN 3.8 7.9 - - - +
17B ASN 3.5 1.8 + - - -
18B ARG 3.3 0.4 - - - -
19B SER* 1.3 75.0 + - - +
21B GLU* 1.3 66.7 + - - +
23B HIS* 3.5 7.0 - - - +
24B ASN* 2.8 26.3 + - - +
35B SER* 3.4 23.6 - - - -
61B TYR* 3.5 20.2 - - + +
87B ARG* 3.4 8.6 - - - +
88B ASN* 3.2 57.0 - - - +
91B ILE* 3.9 23.4 - - + +
92B LYS* 4.0 6.1 - - + -
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Residues in contact with GLU 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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17B ASN* 3.0 22.8 + - - +
18B ARG 3.9 4.3 - - - +
20B MET* 1.3 80.0 - - - +
22B ALA* 1.3 61.4 + - - +
24B ASN* 3.2 7.1 + - - +
25B ILE* 3.1 44.4 + - - +
87B ARG* 3.1 24.7 + - - +
145B HIS 5.2 0.3 - - - +
148B ALA* 3.7 12.8 - - + +
149B THR* 3.5 44.3 + - - +
152B ALA* 3.7 5.4 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.8 24.2 - - + -
18B ARG 3.3 15.6 + - - +
19B SER 3.7 3.4 - - - +
21B GLU* 1.3 76.8 - - - +
23B HIS* 1.3 67.9 + - - +
25B ILE* 3.4 1.3 + - - -
26B LEU* 3.1 36.3 + - + +
152B ALA* 3.7 22.8 - - + +
155B ILE* 4.4 10.5 - - + -
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Residues in contact with HIS 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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10B VAL* 5.0 0.6 - - - +
19B SER 2.7 22.5 + - - +
20B MET* 3.3 12.7 + - - +
22B ALA* 1.3 71.4 - - - +
24B ASN* 1.3 58.0 + - - +
27B SER* 3.0 40.8 + - - -
33B VAL* 3.7 33.6 + - + +
34B ARG* 4.2 8.7 - - - -
35B SER* 2.7 38.8 + - - -
91B ILE* 3.7 33.9 - - + +
92B LYS* 4.6 8.3 - - + -
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Residues in contact with ASN 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 MET 2.8 17.8 + - - +
21B GLU* 3.4 9.8 - - - +
22B ALA 3.1 0.2 - - - -
23B HIS* 1.3 77.5 - - - +
25B ILE* 1.3 68.2 + - + +
27B SER* 3.9 3.8 + - - -
28B LYS* 3.1 56.5 + - - +
87B ARG* 4.2 19.2 + - - +
91B ILE* 3.7 26.7 - - + +
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Residues in contact with ILE 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 GLU* 3.1 32.5 + - - +
22B ALA* 3.9 2.9 - - - +
24B ASN* 1.3 77.1 - - + +
26B LEU* 1.3 69.6 + - + +
27B SER 3.2 0.2 + - - -
28B LYS* 3.3 9.3 + - + +
29B ARG* 2.9 41.8 + - - +
152B ALA* 3.7 21.5 - - + +
153B PHE* 4.0 37.2 - - + -
156B CYS* 4.1 17.9 - - + -
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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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8B VAL* 4.4 9.2 - - + -
10B VAL* 3.8 27.6 - - + -
22B ALA* 3.1 20.1 + - - +
25B ILE* 1.3 80.0 - - + +
27B SER* 1.3 63.0 + - - +
29B ARG* 3.0 12.2 + - - +
30B GLY 3.3 0.2 + - - -
31B PHE* 3.1 51.2 + - + +
33B VAL* 3.9 22.0 - - + -
152B ALA 5.6 0.9 - - - +
155B ILE* 4.0 13.5 - - + -
156B CYS* 3.9 28.3 - - + -
159B CYS* 4.1 11.7 - - - -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 3.0 29.9 + - - -
24B ASN* 3.9 4.6 + - - -
26B LEU* 1.3 75.9 - - - +
28B LYS* 1.3 65.6 + - - +
30B GLY* 3.1 15.2 + - - -
31B PHE 4.2 7.0 + - - +
33B VAL* 3.8 15.5 - - - -
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Residues in contact with LYS 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 ASN* 3.1 44.7 + - - +
25B ILE* 3.6 7.2 - - + +
27B SER* 1.3 79.5 + - - +
29B ARG* 1.3 61.4 + - + +
30B GLY 3.2 3.0 + - - -
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Residues in contact with ARG 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 ILE* 2.9 25.4 + - - +
26B LEU* 3.0 7.3 + - - +
28B LYS* 1.3 80.0 - - + +
30B GLY* 1.3 58.8 + - - +
31B PHE* 3.4 18.0 + - + -
153B PHE* 3.5 40.1 - - - -
156B CYS* 3.8 25.4 - - - -
160B GLN* 4.9 5.2 - - - +
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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