Contacts of the helix formed by residues 55 - 65 (chain A) in PDB entry 1XT9
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 SER 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLY* 5.0 2.2 - - - -
36A PHE* 4.2 6.9 - - - +
53A PHE 3.8 3.6 + - - -
54A ILE* 1.3 73.3 - - - +
56A PRO* 1.3 64.0 - - - -
57A GLU* 3.4 11.1 + - - +
58A VAL* 3.3 28.6 + - - +
59A THR* 2.6 39.2 + - - -
48B LYS* 5.3 0.2 - - - -
49B GLN* 3.6 31.5 + - - +
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Residues in contact with PRO 56 (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 ASP* 3.8 15.9 - - + +
32A ILE* 3.8 26.9 - - + -
33A GLY* 4.2 14.4 - - - +
36A PHE* 5.1 1.3 - - + -
55A SER* 1.3 85.2 - - - +
57A GLU* 1.3 67.9 + - - +
59A THR* 3.6 0.9 - - - -
60A GLN* 2.8 31.9 + - - +
89A ALA* 3.8 26.1 - - + +
91A ASN* 5.8 0.5 - - - +
103A TRP* 3.6 26.6 - - + -
73B LEU* 3.8 5.5 - - + +
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Residues in contact with GLU 57 (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 ASP* 4.2 20.4 - - + +
30A HIS* 4.6 8.0 + - - -
55A SER* 3.4 6.7 - - - +
56A PRO* 1.3 92.6 - - - +
58A VAL* 1.3 58.5 + - - +
60A GLN* 3.6 3.0 + - - +
61A PHE* 3.0 25.6 + - - +
42B ARG* 3.7 37.9 - - + +
44B ILE* 3.9 13.0 - - + -
49B GLN* 3.6 27.3 - - + +
70B VAL* 3.8 30.5 - - + +
73B LEU* 4.6 1.3 - - + -
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Residues in contact with VAL 58 (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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54A ILE* 3.5 21.5 - - + -
55A SER* 3.2 21.1 + - - +
57A GLU* 1.3 73.9 - - - +
59A THR* 1.3 60.9 + - - +
61A PHE* 3.1 7.6 + - - +
62A ILE* 2.9 42.8 + - + +
74A PHE* 3.9 24.9 - - + -
75A LEU* 4.6 5.8 - - + -
78A LEU* 5.2 0.9 - - + -
44B ILE* 3.8 21.8 - - + -
47B GLY 3.9 21.5 - - - +
48B LYS* 4.0 6.5 - - - -
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Residues in contact with THR 59 (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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54A ILE* 3.3 20.3 + - - +
55A SER 2.6 24.8 + - - -
56A PRO 3.6 1.6 - - - -
58A VAL* 1.3 77.1 - - - +
60A GLN* 1.3 63.4 + - - +
62A ILE* 3.0 12.8 + - - +
63A LYS* 2.9 21.7 + - - +
88A LEU* 3.9 13.9 - - + +
89A ALA 3.4 30.9 + - - +
90A ILE* 3.6 26.9 - - + -
91A ASN 5.5 0.7 - - - +
132A VAL* 4.4 5.8 - - + -
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Residues in contact with GLN 60 (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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56A PRO 2.8 18.3 + - - +
57A GLU 3.7 4.7 - - - +
59A THR* 1.3 78.2 - - - +
61A PHE* 1.3 55.6 + - - +
63A LYS* 3.1 29.0 + - - -
64A CYS* 2.8 48.3 + - - -
91A ASN* 4.1 9.8 + - + +
93A ASN* 2.9 25.2 + - - +
95A ASN 4.2 9.5 + - - -
8B LEU* 3.8 18.9 - - + +
70B VAL* 4.3 4.0 - - + -
73B LEU* 3.6 36.9 - - + +
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Residues in contact with PHE 61 (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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57A GLU 3.0 14.7 + - - +
58A VAL 3.1 7.6 + - - +
60A GLN* 1.3 75.4 - - - +
62A ILE* 1.3 71.5 + - + +
65A THR* 2.9 65.3 + - + -
70A GLU* 4.8 0.7 - - + -
71A ILE* 4.5 19.5 - - + -
74A PHE* 3.8 33.4 - + + -
8B LEU* 3.5 28.9 - - + +
44B ILE* 3.6 21.3 - - + -
68B HIS* 3.4 44.6 - + + -
70B VAL* 5.3 0.2 - - + -
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Residues in contact with ILE 62 (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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54A ILE* 5.1 2.0 - - + -
58A VAL* 2.9 32.5 + - + +
59A THR* 3.1 11.9 - - - +
61A PHE* 1.3 93.1 - - + +
63A LYS* 1.3 63.7 + - - +
65A THR 3.7 4.0 - - - +
71A ILE* 5.3 8.2 - - + +
75A LEU* 3.9 38.6 - - + -
88A LEU* 5.0 8.3 - - + -
132A VAL* 4.1 25.8 - - + +
135A LYS* 3.2 29.7 + - + +
136A LEU* 4.2 20.2 - - + -
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Residues in contact with LYS 63 (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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59A THR* 2.9 11.1 + - + +
60A GLN* 3.1 18.3 + - - +
62A ILE* 1.3 77.3 - - - +
64A CYS* 1.3 69.3 + - - +
66A SER* 5.1 0.2 - - - -
90A ILE* 5.5 0.7 - - + -
91A ASN 2.9 26.0 + - - +
93A ASN 3.1 21.6 + - - -
94A SER* 4.7 2.5 + - - +
128A HIS* 3.5 37.1 + - + +
131A GLN* 3.1 45.9 + - + +
132A VAL* 3.5 25.6 - - + -
135A LYS* 3.2 22.9 - - - -
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Residues in contact with CYS 64 (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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60A GLN* 2.8 51.3 + - - +
61A PHE 4.5 0.2 - - - +
63A LYS* 1.3 82.5 - - - +
65A THR* 1.3 60.4 + - - +
66A SER* 3.0 11.6 + - - -
67A ASN* 4.4 3.5 + - - +
93A ASN 4.7 2.5 - - - -
94A SER* 5.6 5.4 - - - -
95A ASN 5.5 3.4 - - - -
131A GLN* 4.9 2.7 - - - +
8B LEU* 4.0 29.3 - - + +
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Residues in contact with THR 65 (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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61A PHE* 2.9 54.2 + - + -
62A ILE* 3.7 4.2 - - - +
64A CYS* 1.3 72.7 - - - +
66A SER* 1.3 56.3 + - - +
67A ASN* 2.8 47.9 + - + +
70A GLU* 3.9 10.1 - - + +
71A ILE* 5.4 12.0 - - + +
135A LYS* 3.2 11.4 + - - -
7B THR 5.3 0.2 + - - -
8B LEU* 3.7 13.3 + - - +
68B HIS* 5.5 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