Contacts of the helix formed by residues 30 - 44 (chain A) in PDB entry 1XGS
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A MET 3.5 1.4 + - - +
29A LEU* 1.3 71.2 - - - +
31A LEU* 1.3 57.9 + - - +
33A LEU* 3.2 4.5 + - + -
34A ALA 2.8 26.3 + - - -
54A LEU* 3.3 35.9 - - + +
56A ILE* 3.8 13.5 - - + -
63A TYR* 3.9 24.7 - - + -
65A PRO* 3.5 14.7 - - + +
69A ASP* 4.6 1.3 - - - +
71A THR* 2.9 44.9 + - + +
73A LEU* 3.7 35.7 - - + +
79A LEU* 4.4 2.9 - - + -
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Residues in contact with LEU 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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29A LEU* 3.1 10.6 - - + +
30A LEU* 1.3 80.4 - - - +
32A GLU* 1.3 61.7 + - + +
34A ALA* 3.9 0.2 - - - +
35A GLU* 3.0 43.3 + - + +
65A PRO* 3.7 14.0 - - + +
66A TYR 3.7 20.6 - - - +
67A LYS* 4.0 24.2 - - + +
68A GLY 4.0 7.6 - - - +
69A ASP* 4.2 17.1 + - + +
71A THR 4.7 0.6 + - - -
238A ARG* 3.5 32.8 - - - +
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Residues in contact with GLU 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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27A GLY 5.1 1.2 - - - +
28A MET* 3.9 16.6 - - - +
29A LEU* 3.1 45.7 + - + +
31A LEU* 1.3 79.0 - - + +
33A LEU* 1.3 62.3 + - - +
35A GLU* 3.5 4.6 + - - +
36A SER* 2.8 32.9 + - - +
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Residues in contact with LEU 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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20A ALA* 4.2 10.1 - - + +
23A LEU* 3.6 36.1 - - + +
24A ALA* 4.4 6.3 - - + -
28A MET* 4.0 11.6 - - + -
29A LEU 2.9 13.2 + - - +
30A LEU* 3.5 11.7 - - + +
32A GLU* 1.3 77.7 - - - +
34A ALA* 1.3 62.1 + - - +
36A SER* 3.4 3.0 + - - -
37A ILE* 3.1 39.3 + - + +
54A LEU* 4.1 18.6 - - + -
73A LEU* 4.0 26.5 - - + -
79A LEU* 4.1 17.0 - - + -
81A ILE* 5.5 1.1 - - + -
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Residues in contact with ALA 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 LEU 2.8 20.1 + - - +
31A LEU 3.9 3.1 - - - +
33A LEU* 1.3 71.4 - - - +
35A GLU* 1.3 63.0 + - - +
37A ILE* 3.7 1.0 - - - +
38A GLU* 3.0 31.9 + - - +
52A VAL* 4.4 13.9 - - + -
54A LEU* 3.7 16.3 - - + +
65A PRO* 3.8 11.2 - - + -
238A ARG* 3.8 25.6 - - - +
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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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31A LEU* 3.0 35.0 + - + +
32A GLU* 3.9 5.2 - - - +
34A ALA* 1.3 76.0 - - - +
36A SER* 1.3 56.3 + - - +
38A GLU* 4.8 0.2 - - - -
39A LYS* 2.9 59.8 + - - +
67A LYS* 3.6 24.7 + - - +
238A ARG* 3.0 34.2 + - - +
239A TRP* 5.4 0.5 - - - -
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Residues in contact with SER 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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19A LYS* 6.4 1.1 - - - -
23A LEU* 4.4 20.2 - - - +
28A MET* 6.2 0.3 - - - +
32A GLU* 2.8 24.6 + - - +
33A LEU* 3.8 4.2 - - - -
34A ALA 3.3 0.2 - - - -
35A GLU* 1.3 72.6 - - - +
37A ILE* 1.3 63.3 + - - +
39A LYS* 3.4 4.9 + - - +
40A MET* 2.9 32.5 + - - +
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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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16A VAL* 3.2 29.7 - - + +
20A ALA* 3.4 40.8 - - + +
23A LEU* 4.6 6.1 - - + -
33A LEU* 3.1 27.7 + - + +
34A ALA* 3.7 4.7 - - - +
36A SER* 1.3 75.8 - - - +
38A GLU* 1.3 63.3 + - - +
40A MET* 3.1 17.7 + - + +
41A ILE* 3.0 26.8 + - + +
52A VAL* 3.4 29.4 - - + -
54A LEU* 6.1 0.2 - - + -
81A ILE* 5.7 0.2 - - + -
83A VAL* 4.1 8.5 - - + -
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Residues in contact with GLU 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 ALA 3.0 17.6 + - - +
37A ILE* 1.3 76.9 - - - +
39A LYS* 1.3 73.7 + - - +
41A ILE* 3.3 11.4 + - + +
42A MET* 3.2 27.0 + - - +
48A PRO* 4.5 15.9 - - + +
51A PRO* 3.5 3.6 - - - +
52A VAL* 2.9 35.4 + - + +
238A ARG* 2.9 45.0 + - - -
239A TRP* 3.0 20.7 + - - -
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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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35A GLU* 2.9 68.6 + - - +
36A SER* 3.8 5.8 - - - +
38A GLU* 1.3 87.1 + - - +
40A MET* 1.3 67.3 + - - +
42A MET* 3.1 16.8 + - + +
43A GLU* 2.9 36.5 + - + +
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Residues in contact with MET 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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15A LYS* 4.9 1.6 - - - +
16A VAL* 3.8 23.6 - - + -
19A LYS* 3.1 63.3 - - + +
23A LEU* 5.7 0.4 - - + -
36A SER* 2.9 15.6 + - - +
37A ILE* 3.1 23.3 + - + +
39A LYS* 1.3 77.2 - - - +
41A ILE* 1.3 62.8 + - - +
43A GLU* 3.0 18.7 + - - +
44A LEU* 2.9 36.7 + - + +
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Residues in contact with ILE 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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12A ILE* 4.2 3.5 - - + +
16A VAL* 3.7 28.7 - - + -
37A ILE* 3.0 21.1 + - + +
38A GLU* 3.5 15.3 - - - +
39A LYS 3.2 0.2 - - - -
40A MET* 1.3 77.9 - - - +
42A MET* 1.3 60.2 + - + +
44A LEU* 3.4 3.6 + - - +
45A GLY 3.3 4.3 + - - -
46A GLY* 2.9 41.9 + - - +
47A LYS* 3.9 10.8 - - - -
48A PRO* 4.0 11.4 - - + -
50A PHE 5.9 0.4 - - - +
52A VAL* 4.8 6.7 - - + -
83A VAL* 5.2 4.3 - - + -
84A GLY 4.0 18.6 - - - +
85A VAL* 3.8 25.6 - - + -
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Residues in contact with MET 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 GLU* 3.2 18.2 - - - +
39A LYS* 3.1 17.6 + - + +
41A ILE* 1.3 74.4 - - - +
43A GLU* 1.3 63.7 + - - +
45A GLY* 3.2 13.0 + - - -
46A GLY 3.3 10.7 - - - +
47A LYS* 3.9 21.1 - - + -
48A PRO* 3.8 28.3 - - + -
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Residues in contact with GLU 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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19A LYS* 5.4 4.0 + - - -
39A LYS* 2.9 29.3 + - + +
40A MET* 3.0 21.7 + - - +
42A MET* 1.3 77.2 - - - +
44A LEU* 1.3 64.1 + - + +
45A GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 44 (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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8A LYS* 4.4 8.1 + - - -
12A ILE* 3.6 44.0 - - + +
15A LYS* 4.2 33.7 - - + +
16A VAL* 3.7 21.1 - - + -
40A MET* 2.9 25.7 + - + +
41A ILE 3.8 4.9 - - - +
42A MET 3.2 0.2 - - - -
43A GLU* 1.3 77.8 - - + +
45A GLY* 1.3 57.7 + - - +
46A GLY 3.7 0.2 - - - -
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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