Contacts of the helix formed by residues 21 - 31 (chain A) in PDB entry 1XFS
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 PRO 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A VAL* 1.3 94.4 - - + +
22A VAL* 1.3 64.7 + - - +
23A ASN* 3.1 21.3 - - - +
24A LEU* 3.2 27.7 + - + -
25A VAL* 3.2 17.5 + - - +
126A GLY* 4.7 5.4 - - - +
127A THR* 3.2 0.4 - - - +
168A LYS* 4.4 14.8 - - - -
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Residues in contact with VAL 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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21A PRO* 1.3 72.5 - - - +
23A ASN* 1.3 61.5 + - + +
25A VAL* 3.8 1.4 - - - +
26A TRP* 2.9 28.2 + - - +
83A GLU* 3.4 44.9 - - + +
120A LEU* 4.0 20.6 - - + -
122A PRO* 4.4 28.6 - - + +
126A GLY 4.7 1.2 + - - -
127A THR* 3.0 22.6 + - + +
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Residues in contact with ASN 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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21A PRO* 3.1 26.7 - - - +
22A VAL* 1.3 82.3 - - + +
24A LEU* 1.3 80.3 + - - +
26A TRP* 3.5 3.1 + - - +
27A ARG* 3.2 30.3 + - - +
83A GLU* 3.6 28.9 - - - +
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Residues in contact with LEU 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* 3.5 18.8 - - + -
21A PRO* 3.2 29.0 + - + +
23A ASN* 1.3 93.0 + - - +
25A VAL* 1.3 65.1 + - - +
27A ARG* 3.1 26.5 + - + +
28A GLY 3.0 16.8 + - - -
164A LEU* 3.7 20.4 - - + +
168A LYS* 3.7 43.1 - - + +
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Residues in contact with VAL 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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18A LEU* 4.5 13.9 - - + -
20A VAL* 3.9 17.5 - - + +
21A PRO 3.2 13.8 + - - +
22A VAL* 3.8 8.1 - - - +
24A LEU* 1.3 75.3 - - - +
26A TRP* 1.3 65.5 + - - +
28A GLY* 3.0 3.3 + - - -
29A LEU* 3.0 28.7 + - + +
120A LEU* 3.7 30.3 - - + -
127A THR* 3.7 19.5 - - + +
129A TYR* 5.0 3.6 - - + -
160A LEU* 4.6 12.8 - - + +
164A LEU* 3.6 12.3 - - + +
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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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22A VAL 2.9 18.3 + - - +
23A ASN 3.6 5.6 - - - +
24A LEU 3.2 0.4 - - - -
25A VAL* 1.3 78.0 - - - +
27A ARG* 1.3 64.6 + - + +
29A LEU* 3.2 8.5 + - + +
30A THR* 2.8 50.3 + - + +
53A LEU* 4.6 5.4 - - + +
80A VAL* 3.8 13.5 - - + -
81A THR 3.5 22.0 - - - -
82A ASP* 3.7 28.2 + - + +
83A GLU* 3.2 39.5 - - + +
84A LYS 4.0 4.5 - - - -
85A ARG* 3.6 15.7 - - - -
86A LEU* 3.9 29.2 - - + -
118A ILE* 5.8 0.4 - - + -
120A LEU* 3.9 14.8 - - + +
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Residues in contact with ARG 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 ASN* 3.2 17.4 + - - +
24A LEU* 3.1 26.9 + - + +
26A TRP* 1.3 81.2 - - + +
28A GLY* 1.3 58.8 + - - +
30A THR* 3.8 6.1 - - - -
31A GLU* 2.7 72.8 + - - +
34A LEU* 3.7 11.0 - - + +
164A LEU* 5.8 0.2 - - + -
170A TYR 6.0 2.4 + - - -
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Residues in contact with GLY 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 LEU 3.0 13.0 + - - -
25A VAL 3.0 4.7 + - - -
27A ARG* 1.3 79.9 - - - +
29A LEU* 1.3 59.1 + - - +
30A THR 3.6 0.3 + - - -
34A LEU* 3.8 17.4 - - - +
35A LEU* 3.5 11.8 + - - +
38A TRP* 2.9 25.8 + - - -
160A LEU* 4.1 15.7 - - - -
164A LEU* 4.3 3.1 - - - -
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Residues in contact with LEU 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 VAL* 3.0 26.1 + - + +
26A TRP* 3.2 12.8 + - + +
28A GLY* 1.3 76.3 - - - +
30A THR* 1.3 62.5 + - + +
35A LEU* 3.6 17.9 - - + +
38A TRP* 3.6 28.9 - - + -
39A PHE* 6.3 0.2 - - + -
59A PHE* 5.4 2.6 - - - -
77A PHE* 5.7 2.4 - - - -
86A LEU* 3.9 20.7 - - + +
88A TRP* 5.1 8.9 - - + -
118A ILE* 3.9 30.5 - - + -
120A LEU* 4.0 23.6 - - + -
129A TYR* 4.2 16.8 - - + +
160A LEU* 4.7 3.4 - - + -
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Residues in contact with THR 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* 2.8 43.5 + - + +
27A ARG* 3.7 6.6 + - - -
29A LEU* 1.3 85.2 - - + +
31A GLU* 1.3 64.1 + - - +
32A PRO* 3.5 10.6 - - - +
35A LEU* 4.1 4.9 - - - -
51A VAL* 3.6 16.1 - - - +
53A LEU* 3.6 42.0 - - + +
77A PHE* 6.1 0.7 - - - -
86A LEU* 4.1 10.8 - - + -
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Residues in contact with GLU 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 ARG* 2.7 70.0 + - - +
29A LEU 3.9 0.6 - - - -
30A THR* 1.3 82.7 - - - +
32A PRO* 1.3 61.0 - - + +
33A GLU* 3.2 6.1 - - + +
34A LEU* 2.8 23.7 + - + +
35A LEU* 2.8 32.9 + - - +
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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