Contacts of the strand formed by residues 25 - 35 (chain A) in PDB entry 3HXG
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 5.1 7.6 - - + -
23A PRO 3.4 9.8 - - - +
24A HIS* 1.3 83.7 - - + +
26A LEU* 1.3 64.5 + - - +
54A SER* 3.7 9.6 - - - +
55A THR* 4.4 3.6 - - + -
6C ILE* 3.5 18.6 - - + +
8C TYR* 2.6 32.3 + - - +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A PRO* 1.3 78.1 - - - +
27A GLN* 1.3 67.5 + - - +
28A ASP* 3.3 23.0 + - - +
30A TRP* 4.1 5.6 - - + -
53A PHE* 3.7 36.3 - - + -
54A SER* 3.1 11.3 + - - +
55A THR 3.7 19.7 - - - +
56A ILE* 3.8 24.0 - - + +
122A ILE* 3.7 39.5 - - + +
6C ILE* 4.0 8.6 - - - +
8C TYR* 4.0 9.4 - - + -
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Residues in contact with GLN 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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26A LEU* 1.3 73.7 - - - +
28A ASP* 1.3 74.8 + - - +
122A ILE 4.6 5.3 + - - +
124A SER* 4.3 8.1 - - - -
132A ASP* 4.1 18.0 + - - +
4C GLY 3.9 2.5 + - - +
5C ARG* 3.4 23.2 - - + +
6C ILE* 2.7 62.1 + - - +
8C TYR* 5.3 0.2 - - - -
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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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26A LEU* 3.3 20.5 - - - +
27A GLN* 1.3 97.6 + - - +
29A SER* 1.3 66.5 + - - +
30A TRP* 3.2 36.6 - - + +
54A SER* 4.3 3.0 - - - -
82A LYS* 3.4 40.0 + - + +
122A ILE 5.3 0.2 + - - -
132A ASP* 3.9 4.0 - - - +
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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
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28A ASP* 1.3 78.1 + - - +
30A TRP* 1.3 60.8 + - - +
52A THR* 3.5 15.2 - - - +
53A PHE 3.4 8.7 + - - -
54A SER* 4.1 15.6 + - - -
82A LYS* 3.5 6.6 - - - +
83A SER* 2.9 38.7 + - - -
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Residues in contact with TRP 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 LEU* 4.1 4.1 - - + +
28A ASP* 3.2 31.1 + - + +
29A SER* 1.3 73.0 + - - +
31A SER* 1.3 59.9 + - - +
52A THR* 3.3 2.9 - - - -
53A PHE* 2.9 71.0 + + + -
80A MET* 3.7 25.4 - - + -
81A PHE* 3.3 10.1 - - - -
82A LYS* 3.3 48.9 - - + -
83A SER* 3.1 6.7 + - - -
121A LEU* 3.6 35.4 - - + -
122A ILE* 3.8 18.8 + - + +
132A ASP* 5.7 1.8 - - - -
135A ILE* 3.8 21.1 - - + -
136A CYS 3.8 8.5 - - - -
137A GLY* 4.1 2.2 - - - -
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Residues in contact with SER 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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30A TRP* 1.3 71.9 - - - +
32A TYR* 1.3 61.0 + - - +
33A TYR* 3.4 32.4 + - - -
49A LYS* 3.9 9.7 + - - +
51A ALA 3.3 7.9 - - - -
52A THR* 2.8 22.5 + - - -
53A PHE* 5.2 0.2 - - - -
80A MET* 3.4 6.3 - - - +
81A PHE 2.7 35.1 + - - -
83A SER* 2.9 22.1 + - - -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A SER* 1.3 72.5 - - - +
33A TYR* 1.3 61.2 + - - +
34A LEU* 4.5 2.2 - - + -
49A LYS* 3.6 2.3 - - - -
50A VAL* 2.7 47.1 + - + +
51A ALA* 2.7 19.8 + - + +
53A PHE* 4.6 7.9 - + + -
59A PHE* 6.3 0.2 - + - -
62A VAL* 3.8 25.4 - - + -
63A LEU* 3.6 17.2 - - + +
66A THR* 3.9 20.0 + - + -
67A VAL 5.0 2.6 + - - -
78A LEU* 3.6 28.4 - - + +
79A TYR 3.5 2.2 - - - -
80A MET* 4.0 23.1 - - + -
114A TRP* 3.0 29.6 + + - -
118A LEU* 4.0 21.5 - - + -
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Residues in contact with TYR 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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31A SER* 3.4 36.6 - - - -
32A TYR* 1.3 76.7 - - - +
34A LEU* 1.3 67.5 + - - +
47A LEU* 4.3 15.5 - - + -
48A GLU* 3.2 10.5 - - - +
49A LYS* 3.5 48.4 + - + -
78A LEU* 3.6 5.7 - - - +
79A TYR* 2.8 49.5 + - + +
81A PHE* 4.6 8.5 - - + -
83A SER 4.5 5.9 + - - -
85A ILE 4.3 6.6 + - - -
86A MET* 4.8 2.8 - - - +
87A PRO* 3.7 41.4 - - + +
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Residues in contact with LEU 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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32A TYR* 4.5 6.7 - - + -
33A TYR* 1.3 75.0 - - - +
35A PHE* 1.3 59.6 + - - +
36A GLN* 3.9 23.2 + - + +
46A CYS 3.5 3.3 - - - +
47A LEU* 3.5 3.2 - - - -
48A GLU* 3.0 42.1 + - + +
50A VAL* 3.8 34.5 - - + -
66A THR* 5.2 7.2 - - + -
67A VAL* 5.1 9.9 - - + -
77A ASP 3.4 4.7 - - - +
78A LEU* 3.7 25.6 - - + -
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Residues in contact with PHE 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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1A GTA 3.5 36.6 - - - -
33A TYR 4.1 0.4 - - - -
34A LEU* 1.3 72.8 - - - +
36A GLN* 1.3 62.0 + - - +
37A PHE* 4.0 10.5 - - + -
43A TRP* 3.3 48.9 - + - -
46A CYS* 3.3 35.4 - - + -
47A LEU* 3.9 21.7 - - + +
75A GLY 3.8 16.8 - - - -
76A LYS* 3.3 9.4 - - - +
77A ASP* 2.8 47.6 + - + +
79A TYR* 3.9 12.8 - + + -
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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