Contacts of the helix formed by residues 13 - 29 (chain A) in PDB entry 1XYY
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 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.2 13.9 + - - -
11A THR 3.3 2.6 + - - -
12A THR* 1.3 76.4 - - - +
14A ASN* 1.3 59.7 + - - +
16A GLU* 3.7 16.2 - - - +
17A TYR* 2.9 29.8 + - - +
131A ARG* 4.0 6.7 + - - -
149A FMN 3.1 1.0 + - - -
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Residues in contact with ASN 14 (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 THR* 3.4 17.5 + - - +
13A GLY* 1.3 73.0 - - - +
15A THR* 1.3 57.5 + - - +
17A TYR* 3.3 2.5 + - - +
18A THR* 3.0 28.6 + - - -
93A CYS* 3.8 7.0 - - - -
128A GLY 5.0 3.0 + - - -
129A ASP* 5.1 3.9 - - - +
130A PRO* 3.4 27.3 - - + +
131A ARG* 3.4 23.2 + - - -
149A FMN 2.7 45.3 + - - +
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Residues in contact with THR 15 (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 TYR* 4.3 5.4 - - + -
9A GLY 3.8 10.3 - - - +
10A SER* 3.8 3.8 - - - -
14A ASN* 1.3 70.0 - - - +
16A GLU* 1.3 59.8 + - - +
18A THR* 3.4 4.3 + - - -
19A ALA* 2.9 24.6 + - - +
56A GLY 3.8 4.7 - - - +
57A CYS 3.8 20.9 - - - +
58A SER* 3.6 9.2 + - - -
91A PHE* 3.6 21.7 - - + -
92A GLY* 4.5 2.0 - - - -
93A CYS* 3.4 26.4 + - - +
149A FMN 2.8 27.1 + - - -
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.2 48.8 + - + -
10A SER* 3.5 11.0 + - - +
13A GLY* 3.7 16.7 - - - +
14A ASN 3.3 0.2 - - - -
15A THR* 1.3 74.8 - - - +
17A TYR* 1.3 61.8 + - - +
18A THR 3.1 0.2 - - - -
19A ALA* 3.2 3.3 + - - +
20A GLU* 2.7 55.2 + - + +
37A ASP* 5.3 1.5 - - - +
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Residues in contact with TYR 17 (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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13A GLY 2.9 18.8 + - - +
14A ASN 3.6 2.7 - - - +
16A GLU* 1.3 77.7 - - - +
18A THR* 1.3 65.8 + - - +
20A GLU* 3.1 20.3 + - + +
21A THR* 3.0 45.0 + - - -
130A PRO* 3.8 22.9 - - + -
131A ARG* 3.5 61.2 + - + +
134A ARG* 3.4 23.6 + - + +
137A ILE* 4.3 7.2 - - + -
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 3.0 18.0 + - - -
15A THR* 3.4 11.4 - - - -
16A GLU 3.1 0.4 - - - -
17A TYR* 1.3 81.5 - - - +
19A ALA* 1.3 56.0 + - - +
21A THR* 3.3 3.3 + - - -
22A ILE* 3.0 35.3 + - + +
91A PHE* 3.7 22.2 - - + -
93A CYS* 3.3 16.6 - - - -
124A LEU* 4.2 2.9 - - + -
126A ILE* 3.4 20.9 - - + +
130A PRO* 3.4 11.8 - - - +
137A ILE* 3.8 17.0 - - + -
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Residues in contact with ALA 19 (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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6A ILE* 3.7 19.6 - - + +
8A TYR* 3.7 30.1 - - + -
15A THR 2.9 17.4 + - - +
16A GLU 3.2 5.6 + - - +
18A THR* 1.3 74.8 - - - +
20A GLU* 1.3 64.2 + - + +
22A ILE* 3.5 3.6 + - - +
23A ALA* 3.0 24.1 + - - +
35A SER* 4.9 3.0 + - - +
91A PHE* 3.9 15.2 - - + -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 6.2 1.3 - - + -
16A GLU* 2.7 45.5 + - + +
17A TYR* 3.5 25.4 - - + +
19A ALA* 1.3 72.6 - - + +
21A THR* 1.3 59.7 + - - +
23A ALA* 3.3 7.1 + - - +
24A ARG* 2.9 31.1 + - - +
35A SER* 5.8 3.6 - - - +
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 3.0 35.8 + - - -
18A THR 3.5 9.0 - - - -
20A GLU* 1.3 74.2 - - - +
22A ILE* 1.3 65.4 + - - +
24A ARG* 3.3 7.9 + - + +
25A GLU* 3.2 21.5 + - - +
134A ARG* 3.8 15.2 - - + -
137A ILE* 3.6 23.1 - - + -
138A VAL* 3.8 23.5 - - + +
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Residues in contact with ILE 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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6A ILE* 4.2 7.2 - - + -
18A THR* 3.0 25.6 + - + +
19A ALA* 3.9 4.3 - - - +
21A THR* 1.3 76.3 - - - +
23A ALA* 1.3 64.5 + - - +
25A GLU* 3.3 3.2 + - - +
26A LEU* 3.0 24.3 + - + +
54A LEU* 3.6 27.8 - - + -
91A PHE* 3.6 48.7 - - + -
124A LEU* 5.0 0.2 - - + -
137A ILE* 3.6 15.9 - - + -
140A TRP* 3.9 17.3 - - + -
141A ALA* 4.0 20.6 - - + -
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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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6A ILE* 3.5 20.6 - - + -
19A ALA 3.0 18.3 + - - +
20A GLU* 3.6 7.2 - - - +
21A THR 3.2 0.2 - - - -
22A ILE* 1.3 75.8 - - - +
24A ARG* 1.3 60.3 + - - +
26A LEU* 3.8 5.4 - - - +
27A ALA* 2.9 32.4 + - - +
33A VAL* 3.8 12.9 - - + +
35A SER* 4.8 11.0 - - - -
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Residues in contact with ARG 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 GLU 2.9 17.5 + - - +
21A THR* 3.8 8.3 - - + +
22A ILE 3.3 0.2 - - - -
23A ALA* 1.3 76.8 - - - +
25A GLU* 1.3 57.1 + - + +
27A ALA* 3.7 3.9 - - - +
28A ASP* 2.7 74.7 + - - +
138A VAL* 6.5 0.9 - - + -
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Residues in contact with GLU 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 THR 3.2 10.5 + - - +
22A ILE 3.8 7.2 - - - +
24A ARG* 1.3 83.3 - - + +
26A LEU* 1.3 57.8 + - - +
28A ASP* 3.6 10.1 - - + +
29A ALA* 3.1 24.1 + - - +
138A VAL* 4.0 32.3 - - + +
141A ALA* 3.5 17.3 - - + +
142A HIS* 3.0 26.0 - - - +
145A ARG* 2.8 36.6 + - - -
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Residues in contact with LEU 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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4A ALA* 3.8 25.8 - - + -
6A ILE* 4.3 7.6 - - + -
22A ILE* 3.0 23.9 + - + +
23A ALA 3.8 1.3 - - - +
25A GLU* 1.3 86.8 + - - +
27A ALA* 1.3 64.9 + - - +
29A ALA* 3.0 12.3 + - - +
30A GLY 3.4 0.3 + - - -
31A TYR* 3.1 34.6 + - + +
33A VAL* 3.3 15.0 - - + -
52A LEU* 5.0 5.6 - - + -
54A LEU* 3.9 23.8 - - + -
141A ALA* 4.0 13.9 - - + +
144A VAL* 5.5 1.3 - - + -
145A ARG* 3.8 21.8 - - + +
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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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23A ALA 2.9 21.2 + - - +
24A ARG* 3.8 4.9 - - - +
26A LEU* 1.3 72.4 - - - +
28A ASP* 1.3 56.6 + - - +
30A GLY* 2.7 24.8 + - - -
31A TYR 3.5 13.9 - - - +
33A VAL* 3.6 15.6 - - + +
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Residues in contact with ASP 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 ARG* 2.7 54.9 + - - +
25A GLU* 3.6 10.8 - - + +
27A ALA* 1.3 71.8 - - - +
29A ALA* 1.3 58.1 - - - +
30A GLY 3.6 0.7 + - - -
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Residues in contact with ALA 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 GLU 3.1 6.8 + - - +
26A LEU 3.0 8.1 + - - +
27A ALA 3.0 1.4 - - - -
28A ASP* 1.3 76.8 - - - +
30A GLY* 1.3 58.1 + - - +
31A TYR* 3.4 4.9 + - + +
145A ARG* 3.4 47.6 - - - +
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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