Contacts of the helix formed by residues 64 - 76 (chain A) in PDB entry 2H5X
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 ASP 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.7 11.9 - - - +
62A PHE* 3.9 3.5 - - - +
63A PRO* 1.3 84.7 - - - +
65A GLY* 1.3 59.9 + - - +
66A GLU* 3.1 24.9 + - - +
67A THR* 2.5 46.1 + - - -
68A ARG* 3.3 21.8 + - - +
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Residues in contact with GLY 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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47A ILE* 3.9 21.5 - - - +
64A ASP* 1.3 74.2 - - - +
66A GLU* 1.3 67.5 + - - +
67A THR 3.2 0.7 - - - -
68A ARG* 3.8 6.7 - - - +
69A ASP* 2.9 39.3 + - - +
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Residues in contact with GLU 66 (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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64A ASP* 3.1 20.9 + - - +
65A GLY* 1.3 82.9 + - - +
67A THR* 1.3 58.4 + - - +
69A ASP* 3.6 8.1 - - - +
70A LEU 3.1 20.1 + - - -
98A ARG* 3.1 27.0 + - - +
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Residues in contact with THR 67 (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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62A PHE* 3.7 31.6 - - + -
63A PRO* 4.6 9.3 - - + +
64A ASP* 2.5 34.5 + - - -
66A GLU* 1.3 71.2 - - - +
68A ARG* 1.3 65.7 + - - +
70A LEU* 2.8 18.8 + - + +
71A PHE* 3.0 11.3 + - - +
89A LEU* 5.0 10.6 - - + +
94A ALA* 4.0 25.9 - - + +
98A ARG* 4.6 2.4 + - - +
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Residues in contact with ARG 68 (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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3A ALA* 3.5 15.4 + - - +
47A ILE* 2.9 43.2 - - + +
48A THR 3.0 29.8 + - - +
49A ALA* 3.9 4.5 - - + -
62A PHE* 3.4 27.7 - - + -
64A ASP 3.3 13.5 + - - +
65A GLY* 3.8 8.8 - - - +
67A THR* 1.3 78.0 - - - +
69A ASP* 1.3 86.5 + - - +
71A PHE* 3.2 6.4 - - - +
72A LEU* 3.2 37.7 + - - +
11D GLU* 5.2 7.9 + - - -
16D HIS* 6.0 3.2 - - - -
27D ARG* 5.6 5.8 - - - +
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Residues in contact with ASP 69 (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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65A GLY 2.9 23.5 + - - +
66A GLU* 3.6 8.6 - - - +
68A ARG* 1.3 100.7 + - - +
70A LEU* 1.3 67.8 + - - +
72A LEU* 3.1 12.0 + - - +
73A THR* 3.0 26.3 + - - +
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Residues in contact with LEU 70 (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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66A GLU 3.1 13.7 + - - +
67A THR* 2.8 11.3 + - + +
69A ASP* 1.3 76.2 - - - +
71A PHE* 1.3 58.3 + - - +
73A THR* 3.2 13.6 + - + -
74A LEU* 3.0 39.9 + - + +
89A LEU* 4.1 15.9 - - + -
94A ALA* 3.8 36.3 - - + +
97A LEU* 4.6 6.3 - - + -
98A ARG* 3.9 37.0 - - + +
101A LEU* 5.3 5.6 - - + -
127A LEU* 6.5 0.2 - - + -
131A VAL* 4.5 16.2 - - + -
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Residues in contact with PHE 71 (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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49A ALA* 3.9 11.2 - - + -
51A ILE* 3.6 29.2 - - + -
60A TYR* 3.6 28.7 - + + -
62A PHE* 3.4 30.1 - + + -
67A THR 3.0 7.3 + - - +
68A ARG 3.2 9.0 - - - +
70A LEU* 1.3 74.8 - - - +
72A LEU* 1.3 75.5 + - + +
74A LEU* 3.1 13.2 + - - +
75A LEU* 3.1 33.4 + - + +
82A PRO* 3.7 13.9 - - + -
85A ALA* 3.6 28.3 - - + -
86A MET* 3.9 13.5 - - + -
89A LEU* 4.2 11.8 - - + +
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Residues in contact with LEU 72 (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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49A ALA* 3.8 24.5 - - + -
51A ILE* 5.2 3.8 - - + -
68A ARG* 3.2 34.1 + - - +
69A ASP* 3.1 14.0 + - - +
71A PHE* 1.3 85.2 - - + +
73A THR* 1.3 61.1 + - - +
75A LEU* 3.3 29.8 + - + +
76A SER* 3.4 7.6 + - - -
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Residues in contact with THR 73 (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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69A ASP* 3.0 14.4 + - - +
70A LEU* 3.4 15.5 - - + -
71A PHE 3.1 0.2 - - - -
72A LEU* 1.3 74.6 - - - +
74A LEU* 1.3 67.5 + - + +
75A LEU 3.0 1.3 - - - -
76A SER* 2.5 30.2 + - - +
127A LEU* 3.4 31.6 - - + +
130A LYS* 4.5 27.7 + - + +
131A VAL* 5.2 5.2 - - + -
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Residues in contact with LEU 74 (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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70A LEU* 3.0 25.2 + - + +
71A PHE* 3.5 6.5 - - - +
73A THR* 1.3 76.0 - - - +
75A LEU* 1.3 63.0 + - - +
77A VAL* 3.2 15.1 + - - +
80A VAL* 3.6 21.2 - - + +
85A ALA* 3.8 36.6 - - + +
88A ALA* 4.5 2.7 - - + -
89A LEU* 4.1 13.7 - - + -
97A LEU* 3.9 29.4 - - + -
101A LEU* 4.4 15.7 - - + -
123A MET* 3.8 26.1 - - + +
127A LEU* 4.6 9.0 - - + -
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Residues in contact with LEU 75 (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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51A ILE* 3.4 31.9 - - + -
53A ARG* 5.9 2.2 - - - +
71A PHE* 3.1 22.4 + - + +
72A LEU* 3.3 23.6 - - + +
73A THR 3.0 0.6 - - - -
74A LEU* 1.3 78.0 - - - +
76A SER* 1.3 59.0 + - - +
77A VAL 3.1 9.9 + - - +
80A VAL 3.5 9.6 - - - +
81A GLY* 3.5 9.4 - - - -
82A PRO* 3.4 35.7 - - + -
85A ALA* 3.8 11.7 - - + -
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Residues in contact with SER 76 (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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72A LEU 3.4 7.5 + - - -
73A THR* 2.5 26.7 + - - +
75A LEU* 1.3 77.3 - - - +
77A VAL* 1.3 59.5 + - - +
78A SER* 3.8 1.6 + - - -
126A GLU* 5.7 1.2 - - - +
127A LEU* 4.2 7.3 - - - +
130A LYS* 4.4 14.8 + - - -
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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