Contacts of the helix formed by residues 23 - 34 (chain P) in PDB entry 4UJ3
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 GLY 23 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21P GLY 3.1 1.0 - - - -
22P VAL* 1.3 80.6 - - - +
24P LYS* 1.3 55.7 + - - +
26P ASN* 3.2 4.0 + - - +
27P LEU* 2.7 42.9 + - - +
124P ASN* 3.7 9.3 + - - -
200P GNP 3.0 34.0 + - - -
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Residues in contact with LYS 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU* 3.7 23.2 - - + +
17P ILE* 3.4 37.9 - - - +
18P GLY 2.7 25.5 + - - +
19P ASP 2.8 19.0 + - - -
22P VAL* 3.8 10.7 - - + +
23P GLY* 1.3 76.1 - - - +
25P SER* 1.3 63.1 - - - +
27P LEU* 3.0 12.4 + - - +
28P LEU* 2.9 23.2 + - - +
66P ASP* 4.1 8.1 - - - +
67P THR 3.9 14.4 - - - -
69P GLY* 3.7 5.6 - - - -
90P VAL* 4.3 7.4 - - + -
200P GNP 2.9 36.2 + - - +
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Residues in contact with SER 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P LYS* 1.3 72.6 - - - +
26P ASN* 1.3 59.6 + - - +
28P LEU* 3.5 4.7 + - - +
29P SER* 2.9 29.9 + - - -
40P SER* 5.5 2.5 - - - -
43P THR* 2.4 16.1 + - - -
66P ASP* 2.9 17.0 + - - -
200P GNP 2.8 23.4 + - - -
201P MG 2.3 31.0 - - - -
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Residues in contact with ASN 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P GLY 3.7 3.6 - - - +
25P SER* 1.3 75.7 - - - +
27P LEU* 1.3 61.5 + - - +
28P LEU 3.2 0.2 - - - -
29P SER* 3.0 10.7 + - - -
30P ARG* 2.8 33.3 + - - +
36P PHE* 3.2 23.3 - - + -
37P ASN* 3.0 34.2 + - - +
40P SER* 2.9 24.5 + - - -
155P ALA* 3.9 8.7 - - + +
200P GNP 2.9 43.4 + - + +
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Residues in contact with LEU 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU* 5.0 7.0 - - + -
23P GLY 2.7 22.9 + - - +
24P LYS* 3.0 8.0 + - - +
26P ASN* 1.3 71.7 - - - +
28P LEU* 1.3 62.7 + - - +
30P ARG* 3.9 3.3 - - - +
31P PHE* 3.2 24.4 + - - +
88P LEU* 5.9 1.8 - - + -
90P VAL* 3.4 44.9 - - + -
122P VAL* 4.7 6.3 - - + -
124P ASN* 3.4 25.6 - - + +
153P THR* 3.5 19.3 - - + +
155P ALA* 4.1 9.4 - - + +
161P VAL* 4.0 13.3 - - + +
165P PHE* 3.7 16.9 - - + -
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Residues in contact with LEU 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU* 3.7 11.3 - - + +
24P LYS 2.9 11.3 + - - +
25P SER* 3.5 8.5 - - - +
27P LEU* 1.3 74.9 - - - +
29P SER* 1.3 61.4 + - - +
31P PHE* 3.2 4.1 + - - +
32P THR* 2.9 51.9 + - + +
47P GLU* 5.1 8.5 - - + +
48P PHE* 5.0 3.1 - - - +
49P ALA* 4.0 13.5 - - + +
64P ILE* 3.4 44.2 - - + +
66P ASP* 3.7 28.7 - - + +
165P PHE* 4.8 2.2 - - - -
755R VAL* 5.8 2.7 - - + -
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Residues in contact with SER 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P SER 2.9 16.1 + - - -
26P ASN* 3.0 29.3 + - - -
28P LEU* 1.3 75.2 - - - +
30P ARG* 1.3 59.8 + - - +
32P THR* 4.0 5.6 - - - -
33P ARG* 3.1 38.9 + - - +
35P GLU 3.0 28.7 + - - -
36P PHE* 4.5 0.2 - - - -
37P ASN* 5.1 0.5 + - - +
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Residues in contact with ARG 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P ASN 2.8 19.5 + - - +
27P LEU 3.9 3.4 - - - +
29P SER* 1.3 78.0 + - - +
31P PHE* 1.3 58.4 + - - +
34P ASN* 3.0 60.1 + - - +
35P GLU 3.5 7.6 - - - +
36P PHE* 3.3 24.2 - - + +
51P ARG* 5.1 0.7 + - - -
155P ALA* 2.9 20.3 + - + +
156P LEU 3.1 25.6 + - - -
157P ASP 5.0 0.4 - - - -
158P SER* 4.2 21.3 - - - +
161P VAL* 3.5 32.3 - - + -
162P GLU* 6.2 0.2 - - - -
428Q LEU* 6.3 0.2 - - - +
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Residues in contact with PHE 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P LEU 3.2 5.7 + - - +
28P LEU 3.2 4.1 + - - +
30P ARG* 1.3 82.8 - - - +
32P THR* 1.3 65.3 + - + +
34P ASN* 4.5 1.0 + - - +
51P ARG* 2.7 76.3 + - + +
53P ILE* 4.3 16.4 - - + -
62P ALA* 5.2 8.3 - - + -
64P ILE* 3.3 31.4 - - + -
161P VAL* 4.0 13.5 - - + -
162P GLU* 4.2 13.7 - - - -
165P PHE* 3.2 54.7 - + + -
166P GLN* 5.1 2.9 - - + -
169P LEU* 4.9 4.9 - - + -
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Residues in contact with THR 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P LEU* 2.9 30.9 + - + +
29P SER* 3.9 3.8 + - - -
31P PHE* 1.3 90.5 - - + +
33P ARG* 1.3 73.6 + - - +
34P ASN 3.6 0.4 - - - -
49P ALA* 3.5 40.6 - - + +
50P THR 4.2 15.6 - - - +
51P ARG* 4.6 10.2 - - + +
64P ILE* 4.5 1.3 - - + -
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Residues in contact with ARG 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P SER* 3.1 22.0 + - - +
32P THR* 1.3 93.4 + - - +
34P ASN* 1.3 71.6 + - - +
35P GLU* 2.9 43.5 + - + +
755R VAL* 4.7 23.1 - - + +
756R LYS* 5.4 8.4 - - - +
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Residues in contact with ASN 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P SER 3.3 0.2 + - - -
30P ARG* 3.0 53.4 + - - +
31P PHE 4.4 1.2 + - - +
32P THR 3.6 1.6 - - - -
33P ARG* 1.3 78.1 - - - +
35P GLU* 1.3 57.9 + - - +
158P SER* 5.3 2.3 - - - -
162P GLU* 5.6 2.1 - - - +
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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