Contacts of the helix formed by residues 24 - 43 (chain A) in PDB entry 1POP
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 SER 24 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 3.4 10.9 - - - +
22A CYS* 2.9 26.2 + - - -
23A GLY* 1.3 70.7 - - - -
25A CYS* 1.3 57.0 + - - +
26A TRP* 3.1 13.0 - - - +
27A ALA* 2.9 24.1 + - - +
28A PHE* 3.2 18.2 + - - -
50A GLU* 6.2 0.2 - - - -
54A LEU* 4.1 17.5 - - - -
62A GLY 4.7 0.7 - - - -
88A TYR* 2.9 22.2 + - - -
303B AR7 3.6 0.2 + - - -
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Residues in contact with CYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 3.4 20.0 - - - +
23A GLY 3.5 0.4 - - - -
24A SER* 1.3 76.3 - - - +
26A TRP* 1.3 55.5 + - - +
28A PHE* 3.3 8.1 + - - +
29A SER* 2.8 36.7 + - - -
159A HIS* 3.7 6.7 - - + +
160A ALA* 3.4 33.5 - - - +
176A SER* 4.3 0.9 - - - +
302B LEU 3.6 1.6 - - - -
303B AR7 1.8 60.8 + - - +
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Residues in contact with TRP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY 3.3 13.8 + - - -
24A SER* 3.7 6.2 - - - +
25A CYS* 1.3 81.8 - - - +
27A ALA* 1.3 77.5 + - + +
29A SER* 3.7 1.9 - - - -
30A ALA* 3.2 23.7 + - - +
53A LEU 3.5 24.2 - - - -
54A LEU* 3.9 18.8 - - + -
57A ASP* 3.3 25.1 - - + -
60A SER* 3.4 28.9 - - - -
62A GLY* 3.3 30.9 + - - -
66A GLY* 3.3 38.8 - - - +
67A TYR 3.9 9.6 - - - -
68A PRO* 4.0 18.6 - - + +
71A ALA* 4.1 11.2 - - + -
160A ALA* 4.0 11.9 - - + -
302B LEU* 3.5 10.1 - - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 2.9 15.0 + - - +
26A TRP* 1.3 91.8 - - + +
28A PHE* 1.3 68.7 + - - +
29A SER 3.2 0.2 + - - -
30A ALA* 3.2 2.4 + - - +
31A VAL* 3.0 27.4 + - - +
50A GLU* 3.8 30.1 - - + +
53A LEU* 4.1 19.7 - - + -
54A LEU* 4.5 3.8 - - + +
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.5 29.6 - - + -
18A ASN 4.0 7.4 - - - -
19A GLN* 3.6 22.2 - - + -
24A SER* 3.2 35.0 + - - -
25A CYS 3.6 7.0 - - - +
27A ALA* 1.3 80.2 - - - +
29A SER* 1.3 61.0 + - - +
31A VAL* 3.4 3.3 + - - +
32A VAL* 3.2 23.6 + - - +
50A GLU* 3.6 36.3 - - + +
83A ARG* 3.9 2.2 - - - -
88A TYR* 3.6 33.0 - + - -
176A SER* 3.8 28.3 - - - +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A CYS 2.8 20.3 + - - -
26A TRP 3.7 5.4 - - - -
28A PHE* 1.3 70.3 - - - +
30A ALA* 1.3 66.6 + - - +
32A VAL* 3.2 21.4 - - - +
33A THR* 3.5 12.8 + - - +
68A PRO* 5.0 0.2 - - - -
131A SER* 2.8 22.4 + - - -
160A ALA* 3.8 19.3 + - - +
161A VAL* 2.7 32.1 + - - +
162A ALA* 4.3 0.5 - - - +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP 3.2 15.1 + - - +
27A ALA 3.7 4.3 - - - +
29A SER* 1.3 78.0 + - - +
31A VAL* 1.3 61.8 + - - +
33A THR* 2.7 28.0 + - - -
34A ILE* 3.1 12.4 + - + +
53A LEU* 4.1 5.6 - - + -
68A PRO* 4.2 2.9 - - + +
71A ALA* 3.8 25.4 - - + -
72A LEU* 4.0 22.4 - - + +
131A SER* 4.6 2.2 + - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 3.0 17.2 + - - +
28A PHE 3.6 5.2 - - - +
29A SER 3.3 0.2 - - - -
30A ALA* 1.3 74.5 - - - +
32A VAL* 1.3 57.9 + - - +
34A ILE* 3.1 9.8 + - + +
35A GLU* 2.8 58.9 + - + +
48A TYR* 3.5 19.3 - - + +
49A SER 4.1 4.3 - - - +
50A GLU* 3.6 33.9 - - + +
53A LEU* 4.0 17.5 - - + -
80A ILE* 4.4 8.5 - - + -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 5.2 1.4 - - - +
13A VAL* 5.1 5.8 - - + -
28A PHE 3.2 12.7 + - - +
29A SER* 3.2 19.5 - - - +
31A VAL* 1.3 75.0 - - - +
33A THR* 1.3 60.7 + - - +
35A GLU* 3.5 17.1 + - + +
36A GLY* 3.1 18.9 + - - -
129A PRO* 4.4 7.6 - - + +
162A ALA* 3.4 29.6 - - + +
164A VAL* 4.2 18.4 - - + -
174A LYS* 4.4 25.4 - - + +
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER 3.5 11.6 + - - +
30A ALA* 2.7 19.5 + - - -
32A VAL* 1.3 74.4 - - - +
34A ILE* 1.3 59.3 + - - +
36A GLY* 3.2 1.4 + - - -
37A ILE* 2.9 31.7 + - - +
72A LEU* 3.5 11.3 - - - +
128A GLN* 5.5 0.3 + - - +
129A PRO* 3.7 20.0 - - + +
130A VAL* 3.6 9.0 - - - +
131A SER* 3.5 32.5 - - - +
162A ALA* 4.8 2.9 - - + -
207A PHE 4.5 2.2 - - - +
209A PRO* 3.5 26.0 - - - +
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 3.5 22.2 - - + +
31A VAL* 3.5 11.2 - - + +
33A THR* 1.3 76.3 + - - +
35A GLU* 1.3 63.6 + - - +
37A ILE* 3.3 7.9 + - - +
38A ILE* 3.0 34.7 + - + +
48A TYR* 3.9 22.9 - - + -
53A LEU* 5.2 0.4 - - + -
72A LEU* 4.0 17.5 - - + -
75A VAL* 3.6 39.3 - - + -
80A ILE* 4.3 21.1 - - + -
105A ALA* 5.2 2.0 - - + -
107A THR* 5.0 6.7 - - + -
209A PRO* 4.4 7.0 - - + -
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 4.3 7.1 - - - +
13A VAL* 6.2 0.2 - - - -
14A THR* 2.6 35.2 + - + +
17A LYS* 4.3 4.5 + - - -
31A VAL* 2.8 33.1 + - + +
32A VAL* 3.7 17.6 - - - +
34A ILE* 1.3 77.1 - - - +
36A GLY* 1.3 61.0 + - - +
38A ILE* 3.8 2.4 + - - +
39A LYS* 3.3 20.1 + - - +
44A ASN 4.9 1.0 - - - +
45A LEU* 4.4 5.6 - - + +
46A ASN 3.3 21.9 + - - +
47A GLN* 3.2 9.7 - - - +
48A TYR* 3.2 36.8 + - + +
50A GLU* 5.1 0.3 - - - +
83A ARG* 5.4 0.2 - - - -
174A LYS* 4.5 1.7 + - - -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 3.7 19.4 + - - +
32A VAL 3.1 13.3 + - - -
33A THR 3.2 3.1 + - - -
34A ILE 3.1 0.8 - - - -
35A GLU* 1.3 75.6 - - - +
37A ILE* 1.3 63.7 + - - +
39A LYS* 3.2 5.0 + - - +
40A ILE* 3.1 31.7 + - - +
129A PRO* 4.3 14.8 - - - -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR 2.9 18.0 + - - +
34A ILE* 3.5 11.7 - - - +
36A GLY* 1.3 70.6 - - - +
38A ILE* 1.3 72.1 + - + +
40A ILE* 3.2 17.0 + - + +
41A ARG* 3.0 34.5 + - + +
107A THR* 4.5 5.4 - - + -
128A GLN* 3.7 28.2 - - + +
129A PRO* 5.0 1.4 - - - +
209A PRO* 3.9 33.0 - - + +
210A VAL* 5.6 0.2 - - - -
211A LYS* 3.9 27.8 - - + +
431A MOH 4.4 12.1 - - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.0 20.5 + - + +
35A GLU 4.0 3.6 - - - +
37A ILE* 1.3 84.6 - - + +
39A LYS* 1.3 56.3 + - - +
41A ARG* 5.0 0.4 - - - -
42A THR* 2.9 51.0 + - + +
44A ASN 3.6 14.8 - - - +
46A ASN* 4.2 4.9 - - + +
48A TYR* 3.7 31.2 - - + +
105A ALA* 4.1 18.8 - - + -
106A LYS 5.2 1.1 - - - +
107A THR* 5.2 6.5 - - + -
211A LYS* 4.5 23.1 - - + -
429A MOH 4.4 9.4 - - - +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS 4.4 11.2 - - - +
11A GLY* 3.6 26.6 + - - +
12A ALA* 3.7 19.5 - - + -
35A GLU 3.3 11.5 + - - +
36A GLY 3.2 9.7 + - - +
38A ILE* 1.3 76.0 - - - +
40A ILE* 1.3 60.8 + - + +
43A GLY* 2.8 56.7 + - - +
44A ASN 3.5 11.3 + - - +
45A LEU* 4.1 16.8 - - + +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TRP* 3.9 30.5 - - + -
12A ALA* 4.8 4.9 - - + -
36A GLY* 3.1 19.5 + - - +
37A ILE* 3.2 10.7 + - + +
39A LYS* 1.3 78.3 - - + +
41A ARG* 1.3 82.1 + - - +
43A GLY 4.7 0.7 + - - -
127A ASN 3.7 19.3 - - - +
128A GLN* 4.0 17.7 - - + -
129A PRO* 4.2 4.0 - - + -
411A MOH 3.7 14.9 + - - +
431A MOH 4.4 12.1 - - - -
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.0 25.3 + - + +
38A ILE 4.9 0.2 - - - -
40A ILE* 1.3 102.5 + - - +
42A THR* 1.3 67.1 + - + +
43A GLY 3.7 0.2 - - - -
211A LYS* 2.8 46.5 + - + +
212A ASN* 3.7 18.7 + - - +
411A MOH 2.8 36.8 + - - -
431A MOH 3.3 27.8 + - - -
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 2.9 39.9 + - + +
41A ARG* 1.3 84.4 - - + +
43A GLY* 1.3 62.4 + - - +
44A ASN* 3.3 28.4 + - - +
211A LYS* 5.7 5.6 - - + -
429A MOH 3.8 13.3 - - - -
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 2.8 45.7 + - - -
40A ILE 4.6 0.6 + - - -
41A ARG 3.7 0.6 - - - -
42A THR* 1.3 77.4 - - - +
44A ASN* 1.3 61.9 + - - +
45A LEU 4.0 0.5 + - - -
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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
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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