Contacts of the helix formed by residues 64 - 75 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.6 13.6 - - - +
62B PHE* 3.4 1.6 - - - +
63B PRO* 1.3 86.1 - - - +
65B GLY* 1.3 63.3 + - - +
66B GLU* 3.1 25.9 - - - +
67B THR* 2.7 36.1 + - - -
68B ARG* 3.2 16.8 + - - +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 6.0 1.8 - - - -
47B ILE* 3.7 23.7 - - - +
64B ASP* 1.3 74.7 - - - +
66B GLU* 1.3 58.9 + - - +
68B ARG* 3.1 11.2 + - - +
69B ASP* 2.7 44.0 + - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASP* 3.1 32.4 - - - +
65B GLY* 1.3 85.5 + - - +
67B THR* 1.3 61.8 + - - +
69B ASP* 3.3 8.9 + - - +
70B LEU* 3.1 15.8 + - - +
98B ARG* 3.2 27.7 + - - +
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.7 28.3 - - + -
63B PRO* 4.5 10.7 - - + +
64B ASP* 2.7 27.5 + - - -
66B GLU* 1.3 73.1 - - - +
68B ARG* 1.3 61.2 + - - +
70B LEU* 2.9 20.4 + - - +
71B PHE* 3.1 12.1 + - - +
89B LEU* 4.8 10.2 - - + +
94B ALA* 4.1 23.8 - - + +
98B ARG* 3.8 8.5 + - - +
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 4.6 13.7 + - - -
16A HIS* 5.9 2.8 - - - -
18A VAL* 5.8 2.0 - - - +
27A ARG* 5.6 6.5 - - - +
3B ALA* 3.3 17.3 + - - +
47B ILE* 2.9 36.5 - - + +
48B THR 3.0 36.2 + - - +
49B ALA* 4.0 5.4 - - + +
62B PHE* 3.6 25.5 - - + -
64B ASP 3.2 10.0 + - - +
65B GLY* 3.1 16.0 + - - +
67B THR* 1.3 77.0 - - - +
69B ASP* 1.3 82.0 + - - +
71B PHE* 3.2 6.4 + - - +
72B LEU* 3.1 41.7 + - - +
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY 2.7 22.2 + - - +
66B GLU* 3.5 8.5 - - - +
67B THR 3.1 0.2 - - - -
68B ARG* 1.3 97.9 + - - +
70B LEU* 1.3 66.0 + - - +
72B LEU* 3.2 13.3 + - - +
73B THR* 3.0 26.7 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU 3.1 11.6 + - - +
67B THR* 2.9 12.4 + - - +
69B ASP* 1.3 75.3 - - - +
71B PHE* 1.3 64.5 + - - +
73B THR* 3.0 12.7 + - + -
74B LEU* 2.9 49.3 + - + +
89B LEU* 4.1 10.8 - - + -
94B ALA* 3.9 23.3 - - + +
97B LEU* 4.3 8.5 - - + -
98B ARG* 3.6 43.1 - - + +
101B LEU* 5.1 5.8 - - + -
127B LEU* 5.4 0.7 - - + -
131B VAL* 6.2 4.0 - - + -
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 3.9 13.7 - - + -
51B ILE* 3.8 17.9 - - + -
60B TYR* 3.6 35.2 - + + -
62B PHE* 3.3 29.6 - + + -
67B THR 3.1 7.7 + - - +
68B ARG 3.2 8.5 - - - +
70B LEU* 1.3 77.7 - - - +
72B LEU* 1.3 66.9 + - + +
74B LEU* 3.0 21.9 + - - +
75B LEU* 3.2 22.3 + - + +
82B PRO* 3.7 21.1 - - + -
85B ALA* 3.3 33.7 - - + -
86B MET* 3.9 12.1 - - - -
89B LEU* 4.2 11.1 - - + +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 3.8 22.2 - - + -
51B ILE* 5.0 3.8 - - + -
68B ARG* 3.1 40.2 + - - +
69B ASP* 3.6 13.7 - - - +
71B PHE* 1.3 83.0 - - + +
73B THR* 1.3 62.5 + - - +
75B LEU* 3.2 30.5 + - + +
76B SER* 3.5 6.2 + - - -
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASP* 3.0 16.8 + - - +
70B LEU* 3.2 14.7 - - + -
72B LEU* 1.3 75.3 - - - +
74B LEU* 1.3 65.0 + - - +
76B SER* 2.7 30.3 + - - +
77B VAL 4.1 0.2 + - - -
127B LEU* 3.3 33.9 - - + +
130B LYS* 4.3 21.9 - - + +
131B VAL* 5.8 1.6 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 2.9 34.4 + - + +
71B PHE* 3.0 7.8 + - - +
73B THR* 1.3 75.1 - - - +
75B LEU* 1.3 62.5 + - - +
76B SER 3.1 1.0 + - - -
77B VAL* 3.2 13.0 + - - +
80B VAL* 3.2 24.0 - - + +
85B ALA* 3.8 38.6 - - + +
88B ALA* 4.5 5.2 - - + -
89B LEU* 4.1 13.0 - - + -
97B LEU* 4.0 25.4 - - + -
101B LEU* 4.4 7.0 - - + -
123B MET* 5.2 12.8 - - - -
127B LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 4.2 26.0 - - + -
53B ARG* 5.9 3.6 - - - +
71B PHE* 3.5 22.9 - - + +
72B LEU* 3.3 22.4 - - + +
73B THR 3.1 0.6 - - - -
74B LEU* 1.3 77.6 - - - +
76B SER* 1.3 58.1 + - - +
77B VAL 3.1 4.5 + - - +
80B VAL 3.6 13.3 - - - +
81B GLY* 3.4 11.4 - - - +
82B PRO* 3.4 38.4 - - + -
85B ALA* 3.9 10.1 - - + -
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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