Contacts of the helix formed by residues 28 - 47 (chain P) in PDB entry 5G04
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 ASP 28 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PHE 4.1 0.2 - - - -
27P SER* 1.3 84.8 + - - +
29P LEU* 1.3 60.7 + - - +
30P ARG* 3.4 8.1 - - + +
31P GLU* 3.3 24.1 - - + +
32P ILE* 3.0 28.7 + - - +
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Residues in contact with LEU 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P PHE 5.1 1.1 - - - +
27P SER 3.4 17.9 + - - +
28P ASP* 1.3 70.9 - - - +
30P ARG* 1.3 58.1 + - - +
32P ILE* 2.8 14.3 + - + +
33P LYS* 2.6 37.0 + - - +
62P LEU* 3.9 25.0 - - + +
63P PRO* 4.4 19.5 - - + -
257P VAL* 3.2 42.0 - - + +
258P GLY* 4.5 5.8 - - - -
259P PHE* 5.6 2.9 - - + -
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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
----------------------------------------------------------
28P ASP* 5.4 7.0 - - + -
29P LEU* 1.3 77.9 - - - +
31P GLU* 1.3 61.3 + - + +
33P LYS* 4.0 4.5 - - - +
34P LYS* 3.0 30.1 + - - +
63P PRO* 5.9 3.0 - - + +
65P LEU* 4.1 21.2 - - + +
68P ALA 5.5 0.2 - - - -
69P GLU* 3.8 26.8 - - + +
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Residues in contact with GLU 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P ASP* 3.3 27.1 + - + +
30P ARG* 1.3 80.5 - - + +
32P ILE* 1.3 61.4 + - + +
34P LYS* 3.4 27.7 + - - +
35P GLN* 2.9 38.7 + - + +
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Residues in contact with ILE 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P PHE* 3.7 45.8 - - + +
27P SER 5.0 0.4 - - - +
28P ASP 3.0 19.1 + - - +
29P LEU* 2.8 18.2 + - + +
31P GLU* 1.3 70.9 - - + +
33P LYS* 1.3 58.4 + - - +
35P GLN* 3.6 7.7 - - - +
36P LEU* 2.7 34.9 + - + +
62P LEU* 4.1 14.8 - - + -
228P TRP* 3.6 44.4 - - + +
259P PHE* 4.4 11.7 - - + -
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Residues in contact with LYS 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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85C ASP* 2.8 39.4 + - - +
29P LEU 2.6 20.2 + - - +
30P ARG* 4.0 5.4 - - - +
32P ILE* 1.3 73.8 - - - +
34P LYS* 1.3 57.6 + - - +
36P LEU* 3.3 4.3 + - - +
37P LEU* 2.8 41.1 + - + +
59P ALA* 3.6 16.9 - - + +
62P LEU* 3.3 35.8 + - + -
63P PRO* 3.2 28.8 + - + +
64P ALA* 3.3 10.9 - - - +
65P LEU* 4.0 26.6 - - + +
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Residues in contact with LYS 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ARG 3.0 18.1 + - - +
31P GLU* 3.7 32.5 + - - +
33P LYS* 1.3 76.9 - - - +
35P GLN* 1.3 71.4 + - - +
37P LEU* 3.3 7.7 + - - +
38P LEU* 3.1 26.9 + - - +
65P LEU* 4.7 13.4 - - + +
69P GLU* 3.4 28.7 - - + +
70P LEU* 5.7 0.4 - - - -
71P GLN* 3.2 41.3 - - + +
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Residues in contact with GLN 35 (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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31P GLU* 2.9 26.0 + - + +
32P ILE* 3.6 6.3 - - - +
34P LYS* 1.3 85.6 - - - +
36P LEU* 1.3 59.6 + - - +
38P LEU* 3.4 21.7 + - + +
39P ILE* 3.3 19.1 + - - +
201P LEU* 3.6 30.3 - - + +
227P THR* 6.4 0.4 - - - +
228P TRP* 3.5 24.9 + - - -
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Residues in contact with LEU 36 (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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32P ILE 2.7 19.3 + - - +
33P LYS 3.5 4.3 - - - +
35P GLN* 1.3 70.0 - - - +
37P LEU* 1.3 66.2 + - - +
39P ILE* 3.2 15.8 - - + +
40P ALA* 3.1 20.3 + - - +
54P TRP* 4.4 10.5 - - + -
55P SER* 3.5 33.9 - - - +
58P LEU* 3.5 17.7 - - + -
59P ALA* 3.5 29.8 - - + +
62P LEU* 4.3 13.7 - - + -
201P LEU* 5.2 2.7 - - + +
228P TRP* 4.2 25.7 - - + -
229P MET* 5.4 0.9 - - - -
259P PHE* 4.6 2.2 - - + -
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Residues in contact with LEU 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C MET* 4.5 25.8 - - + -
85C ASP* 5.2 4.3 - - - +
88C THR* 3.6 38.4 - - + +
33P LYS* 2.8 38.8 + - - +
34P LYS* 3.5 7.0 - - - +
36P LEU* 1.3 79.3 - - - +
38P LEU* 1.3 62.4 + - - +
40P ALA* 3.3 11.6 + - + +
41P GLY* 3.1 18.9 + - - -
56P ALA* 6.3 0.9 - - + -
59P ALA* 4.2 16.8 - - + -
65P LEU* 4.6 12.6 - - + -
70P LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 38 (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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34P LYS* 3.1 12.2 + - - +
35P GLN* 3.4 29.6 + - + +
36P LEU 3.3 0.2 - - - -
37P LEU* 1.3 75.2 - - - +
39P ILE* 1.3 63.8 + - + +
41P GLY* 3.3 3.7 + - - -
42P LEU* 3.0 57.2 + - + +
71P GLN* 3.8 28.3 - - - +
201P LEU* 5.9 3.1 - - + -
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Residues in contact with ILE 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLN 3.3 6.3 + - - +
36P LEU* 3.2 27.7 + - + +
38P LEU* 1.3 80.1 - - + +
40P ALA* 1.3 64.3 + - - +
42P LEU* 3.3 9.6 + - + -
43P THR* 2.9 38.7 + - + -
55P SER* 4.2 11.9 - - - -
170P PHE* 5.2 2.9 - - + -
199P LEU* 3.8 17.9 - - + -
200P PRO 3.5 24.9 - - - +
201P LEU* 3.3 47.8 - - + +
202P HIS* 3.6 5.4 - - + +
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Residues in contact with ALA 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C THR* 6.0 1.3 - - - -
36P LEU 3.1 11.2 + - - +
37P LEU* 3.5 18.4 - - + +
39P ILE* 1.3 74.5 - - - +
41P GLY* 1.3 56.3 + - - +
43P THR* 3.0 6.9 + - - -
44P ARG* 3.0 37.4 + - - +
52P SER* 3.1 8.2 + - - +
55P SER* 3.2 25.1 - - - +
56P ALA* 4.3 15.9 - - + +
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Residues in contact with GLY 41 (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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37P LEU 3.1 10.6 + - - -
38P LEU* 3.6 4.9 - - - -
39P ILE 3.3 0.4 - - - -
40P ALA* 1.3 78.0 - - - +
42P LEU* 1.4 55.3 - - - +
44P ARG* 3.3 23.7 + - - +
45P GLU* 3.1 33.9 + - - +
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Residues in contact with LEU 42 (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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38P LEU* 3.0 45.3 + - + +
39P ILE* 3.6 14.1 - - + +
41P GLY* 1.4 72.9 - - - +
43P THR* 1.3 62.9 + - - +
45P GLU* 3.5 5.1 + - - +
46P ARG* 3.3 60.6 + - - +
74P PRO* 5.9 7.6 - - + -
170P PHE* 4.1 18.8 - - + -
199P LEU* 5.8 5.2 - - + -
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Residues in contact with THR 43 (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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39P ILE* 2.9 27.1 + - + +
40P ALA* 3.0 7.3 + - - -
42P LEU* 1.3 72.2 - - - +
44P ARG* 1.3 59.6 + - - +
46P ARG* 3.1 7.9 + - - +
47P GLY 2.9 23.7 + - - -
48P LEU* 3.0 15.2 + - + -
51P SER* 3.5 21.4 - - - +
52P SER* 2.3 34.7 + - - -
55P SER* 4.6 1.4 + - - +
170P PHE* 3.7 25.6 - - + -
202P HIS* 4.0 10.8 - - + +
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Residues in contact with ARG 44 (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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45C GLU* 5.6 6.1 + - - -
87C TYR* 5.5 5.3 - - - -
88C THR* 4.2 34.9 + - - +
91C LYS* 3.9 30.9 - - - +
92C ALA* 5.4 8.2 - - - +
95C ASP* 4.8 8.1 - - - +
40P ALA* 3.0 30.3 + - - +
41P GLY* 3.5 19.4 + - - +
43P THR* 1.3 70.6 - - - +
45P GLU* 1.3 70.3 + - + +
47P GLY* 3.1 15.3 + - - +
48P LEU 5.0 0.9 - - - +
49P LEU* 6.0 0.9 - - - +
52P SER* 2.9 17.6 + - - +
91P LYS* 3.7 11.3 + - - +
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Residues in contact with GLU 45 (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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41P GLY 3.1 18.7 + - - +
42P LEU* 3.5 12.4 - - - +
44P ARG* 1.3 78.3 - - + +
46P ARG* 1.3 74.0 + - - +
87P TYR* 2.3 30.0 + - + +
91P LYS* 3.3 14.8 - - - +
113P LYS* 3.1 32.0 + - - +
117P LEU* 4.6 0.3 - - - +
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Residues in contact with ARG 46 (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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42P LEU* 3.3 42.5 + - - +
43P THR* 3.1 10.3 + - - +
45P GLU* 1.3 99.1 + - - +
47P GLY* 1.3 59.8 + - - +
48P LEU* 4.0 8.6 - - + +
87P TYR* 4.4 1.1 - - - -
91P LYS* 4.4 2.0 - - - -
94P PHE* 4.7 1.9 - - - -
112P LYS* 6.1 0.8 - - - +
113P LYS* 3.9 40.8 - - - +
116P PHE* 3.4 44.1 - - + +
117P LEU* 4.0 18.8 - - - +
120P TYR* 4.2 5.7 - - - -
170P PHE* 3.6 33.3 - - + -
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Residues in contact with GLY 47 (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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43P THR 2.9 3.4 + - - -
44P ARG* 3.1 13.9 + - - -
45P GLU 3.3 0.4 - - - -
46P ARG* 1.3 78.8 - - - +
48P LEU* 1.3 63.3 + - - +
49P LEU* 3.2 26.5 + - - +
91P LYS* 4.1 12.8 - - - -
94P PHE* 4.1 12.3 - - - -
120P TYR* 3.7 12.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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