Contacts of the helix formed by residues 19 - 34 (chain A) in PDB entry 1I3D
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS 3.7 3.4 + - - +
18A VAL* 1.3 72.3 - - - +
20A VAL* 1.2 59.6 + - - +
21A GLU* 2.5 35.4 + - - +
22A ASP* 2.8 32.6 + - + +
23A ALA* 2.8 27.9 + - - +
117A HIS* 5.4 10.3 + - + -
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Residues in contact with VAL 20 (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 TRP* 3.9 33.9 - - + +
18A VAL* 3.2 9.0 + - + +
19A ASN* 1.2 76.8 + - - +
21A GLU* 1.4 73.3 + - - +
23A ALA* 4.3 6.1 - - - +
24A GLY* 2.9 21.7 + - - -
65A LYS* 3.9 16.7 - - + +
68A LEU* 3.9 18.4 - - + +
69A THR* 3.8 23.1 - - - +
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Residues in contact with GLU 21 (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 ASN* 2.5 31.6 - - - +
20A VAL* 1.4 81.4 + - - +
22A ASP* 1.3 60.2 - - - +
24A GLY* 4.7 0.7 + - - -
25A GLY 4.9 1.6 + - - -
61A LYS* 2.7 34.5 + - - +
65A LYS* 3.4 42.3 + - + +
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Residues in contact with ASP 22 (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 ASN* 2.8 33.8 + - + +
20A VAL 3.1 0.4 - - - -
21A GLU* 1.3 83.1 - - - +
23A ALA* 1.4 67.5 + - - +
24A GLY 3.2 3.1 + - - -
25A GLY* 3.6 2.8 + - - -
26A GLU* 3.0 42.9 + - - +
61A LYS* 4.5 7.0 + - - +
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Residues in contact with ALA 23 (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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18A VAL* 3.8 16.8 - - + -
19A ASN 2.8 21.7 + - - +
22A ASP* 1.4 74.5 - - - +
24A GLY* 1.4 57.7 + - - +
26A GLU* 3.5 13.8 - - - +
27A THR* 2.8 37.5 + - - +
68A LEU* 3.4 19.5 - - + -
110A LEU* 5.7 1.6 - - + -
113A VAL* 4.8 9.2 - - + -
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Residues in contact with GLY 24 (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 VAL 2.9 17.3 + - - -
22A ASP 3.2 0.2 - - - -
23A ALA* 1.4 79.3 - - - +
25A GLY* 1.3 62.5 + - - +
27A THR* 3.7 2.3 - - - -
28A LEU 3.1 17.5 + - - -
64A GLY* 3.3 36.8 - - - +
65A LYS* 3.8 1.8 - - - -
68A LEU* 3.6 10.8 - - - +
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Residues in contact with GLY 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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21A GLU 4.9 1.8 + - - -
22A ASP 3.6 5.3 + - - -
23A ALA 3.5 0.2 - - - -
24A GLY* 1.3 73.9 - - - +
26A GLU* 1.4 57.6 + - - +
28A LEU 4.7 0.2 - - - -
29A GLY* 2.9 27.7 + - - -
55A MET* 4.1 4.6 - - - +
60A VAL* 4.1 6.7 - - - +
61A LYS* 3.7 40.5 + - - +
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Residues in contact with GLU 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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22A ASP* 3.0 38.3 + - - +
23A ALA* 3.5 15.7 + - - +
24A GLY 3.2 0.4 - - - -
25A GLY* 1.4 59.9 - - - +
27A THR* 1.3 58.2 + - - +
30A ARG* 3.0 32.7 + - - +
55A MET* 4.1 16.0 - - + +
113A VAL* 4.1 21.1 - - + +
117A HIS* 5.6 4.3 + - - +
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Residues in contact with THR 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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23A ALA 2.8 22.4 + - - -
24A GLY 3.7 2.9 - - - -
26A GLU* 1.3 74.2 - - - +
28A LEU* 1.3 65.4 + - - +
30A ARG 3.3 0.7 + - - -
31A LEU* 3.1 20.4 + - - +
68A LEU* 4.2 14.1 - - + +
106A LEU* 3.7 21.8 - - + -
109A VAL* 3.3 16.5 - - + +
110A LEU* 3.9 33.7 - - + +
113A VAL* 3.7 19.8 - - - +
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Residues in contact with LEU 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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24A GLY 3.1 14.5 + - - +
27A THR* 1.3 78.4 - - - +
29A GLY* 1.4 63.2 + - - +
31A LEU* 3.2 17.0 + - + +
32A LEU* 3.0 41.1 + - + +
42A PHE* 4.2 14.1 - - + -
45A PHE* 4.4 6.3 - - + -
60A VAL* 3.5 35.2 - - + +
63A HIS* 3.6 29.6 - - + -
64A GLY* 3.8 9.9 - - - +
67A VAL* 5.4 1.8 - - + -
106A LEU* 4.8 4.9 - - + -
148A CMO 4.0 18.6 - - - +
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Residues in contact with GLY 29 (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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25A GLY 2.9 19.0 + - - -
28A LEU* 1.4 77.8 - - - +
30A ARG* 1.3 61.1 + - - +
32A LEU* 3.2 1.6 + - - -
33A VAL* 2.9 28.2 + - - +
54A ILE* 3.6 14.6 - - - +
55A MET* 3.6 19.5 - - - -
60A VAL* 3.8 7.7 - - - +
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Residues in contact with ARG 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 GLU* 3.0 20.6 + - - +
28A LEU 3.3 0.2 - - - -
29A GLY* 1.3 76.0 - - - +
31A LEU* 1.3 55.7 + - - +
33A VAL 3.3 0.2 + - - -
34A VAL* 2.8 42.3 + - + +
55A MET* 4.0 1.4 - - - -
109A VAL* 3.6 23.8 - - + -
112A THR* 4.4 6.5 - - - -
113A VAL* 4.0 18.4 - - - +
116A ILE* 3.4 19.4 - - - +
120B LYS* 5.8 0.4 + - - +
122B PHE* 3.0 31.2 + - - -
123B THR* 3.5 13.7 + - - +
124B PRO* 3.5 36.7 - - + +
127B GLN* 2.9 34.9 + - - +
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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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27A THR 3.1 12.6 + - - +
28A LEU* 3.4 22.7 - - + +
30A ARG* 1.3 76.3 - - - +
32A LEU* 1.3 63.5 + - + +
35A TYR* 3.0 49.2 + - + +
38A THR* 3.7 27.6 - - + +
42A PHE* 5.3 0.2 - - + -
102A ASN 5.1 1.1 - - - +
105A LEU* 4.1 7.0 - - + -
106A LEU* 4.0 40.4 - - + +
109A VAL* 3.9 20.8 - - + +
147A HEM 4.5 13.5 - - + -
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Residues in contact with LEU 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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28A LEU* 3.0 31.4 + - + +
29A GLY 3.2 4.0 + - - +
31A LEU* 1.3 76.8 - - + +
33A VAL* 1.4 60.6 + - - +
36A PRO* 3.4 9.7 - - - +
38A THR* 3.5 19.1 - - - +
39A GLN* 2.9 40.9 + - + +
42A PHE* 3.8 33.2 - - + -
45A PHE* 5.7 0.2 - - + -
48A LEU* 4.4 11.9 - - + -
54A ILE* 3.9 18.8 - - + -
60A VAL* 4.0 27.8 - - + -
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Residues in contact with VAL 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 GLY 2.9 20.1 + - - +
30A ARG 3.9 0.2 - - - +
32A LEU* 1.4 79.0 - - - +
34A VAL* 1.3 64.8 + - - +
36A PRO* 3.7 11.1 - - - +
39A GLN* 4.9 0.9 - - - +
51A ALA* 4.0 25.1 - - + -
54A ILE* 3.8 27.6 - - + -
55A MET* 4.2 5.6 - - - -
124B PRO* 3.7 39.7 - - + +
125B GLU* 4.2 7.6 - - + +
128B ALA* 4.7 7.6 - - + +
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Residues in contact with VAL 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 ARG* 2.8 29.5 + - + +
33A VAL* 1.3 73.2 - - - +
35A TYR* 1.4 82.2 + - + +
36A PRO* 3.3 6.9 - - - +
37A TRP* 4.9 1.7 - - - -
109A VAL* 5.7 0.4 - - + -
124B PRO* 3.5 26.0 - - + +
127B GLN* 3.9 24.0 - - + +
128B ALA* 4.1 14.5 - - - +
131B GLN* 3.6 33.1 - - + +
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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