Contacts of the helix formed by residues 57 - 69 (chain B) in PDB entry 1X1O
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 GLY 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ALA* 1.4 71.0 - - - +
58B LEU* 1.3 64.4 + - - +
59B TRP* 3.2 3.4 - - - -
60B VAL* 3.0 21.5 + - - +
61B ALA 3.0 10.6 + - - -
80B GLU* 2.7 17.4 + - - -
111B LEU* 3.3 14.3 - - - +
114B LEU* 3.9 20.4 - - - -
151B TYR* 4.3 5.2 - - - -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.6 7.6 - - + -
56B ALA 3.6 0.4 - - - -
57B GLY* 1.3 78.3 - - - +
59B TRP* 1.3 57.7 + - - +
61B ALA* 3.3 1.2 + - - +
62B GLU* 3.0 23.0 + - - +
74B PHE* 3.5 34.0 - - + -
76B PRO* 4.1 10.1 - - + -
78B VAL* 3.6 29.2 - - + +
79B ALA 4.1 2.9 - - - +
80B GLU* 3.0 35.9 + - + +
90B VAL* 3.6 34.1 - - + +
111B LEU* 3.6 14.1 - - + +
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Residues in contact with TRP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 5.6 4.7 - - - -
14B LEU* 3.3 36.3 - - + -
58B LEU* 1.3 76.8 - - - +
60B VAL* 1.3 81.8 + - + +
62B GLU* 3.5 16.7 - - - +
63B ARG* 3.2 48.8 + - + +
80B GLU* 3.8 9.9 - - + -
148B LEU* 4.9 4.3 - - + -
151B TYR* 3.1 52.9 + + + -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.8 1.3 - - + -
18B LEU* 4.1 15.7 - - + +
57B GLY* 3.0 17.0 + - - +
59B TRP* 1.3 115.2 - - + +
61B ALA* 1.3 65.3 + - - +
63B ARG* 3.2 7.1 + - - +
64B VAL* 3.0 21.1 + - - +
110B LEU* 3.9 33.4 - - + -
114B LEU* 4.3 5.6 - - + -
148B LEU* 4.0 21.5 - - + -
151B TYR* 5.4 0.7 - - + -
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Residues in contact with ALA 61 (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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57B GLY 3.0 5.6 + - - +
58B LEU 3.6 7.9 - - - +
60B VAL* 1.3 77.4 - - - +
62B GLU* 1.3 62.1 + - - +
64B VAL* 3.1 10.6 + - - +
65B PHE* 3.0 30.0 + - - -
74B PHE* 4.1 11.9 - - + -
107B ALA* 4.3 14.1 - - + +
110B LEU* 6.0 1.5 - - - +
111B LEU* 3.4 38.8 - - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU 3.0 13.6 + - - +
59B TRP* 3.5 18.9 - - - +
60B VAL 3.2 0.2 - - - -
61B ALA* 1.3 77.7 - - - +
63B ARG* 1.3 59.5 + - + +
65B PHE* 3.3 3.3 + - - +
66B ALA* 2.9 29.3 + - + +
72B THR* 5.2 0.2 + - - -
74B PHE* 3.5 50.0 + - + +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 5.1 9.5 - - - +
14B LEU* 5.4 3.6 - - - +
15B GLU* 4.5 20.2 + - - +
18B LEU* 3.9 18.9 - - + +
59B TRP* 3.2 36.6 + - + +
60B VAL* 3.2 9.2 + - - +
62B GLU* 1.3 79.5 - - + +
64B VAL* 1.3 59.7 + - - +
66B ALA* 3.5 10.4 - - - +
67B LEU* 2.8 40.7 + - + +
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Residues in contact with VAL 64 (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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18B LEU* 4.3 12.3 - - + -
22B LEU* 4.6 5.4 - - + +
60B VAL 3.0 21.3 + - - +
61B ALA 3.1 7.6 + - - +
63B ARG* 1.3 76.2 - - - +
65B PHE* 1.3 62.5 + - - +
67B LEU* 3.2 10.5 + - - +
68B ALA* 3.0 20.6 + - - +
103B GLY* 3.6 28.9 - - - +
106B LEU* 4.0 19.5 - - + -
107B ALA* 3.8 17.9 - - + +
110B LEU* 4.0 25.8 - - + -
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Residues in contact with PHE 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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47B ILE* 4.4 7.9 - - + -
61B ALA 3.0 22.2 + - - -
62B GLU* 3.8 6.3 - - - +
64B VAL* 1.3 76.2 - - - +
66B ALA* 1.3 62.7 + - - +
68B ALA* 3.3 6.8 + - - +
69B ASP 3.0 17.2 + - - -
72B THR* 3.0 25.9 + - + +
74B PHE* 3.9 31.9 - + + -
93B VAL* 4.1 13.9 - - + -
99B GLY 4.3 1.1 - - - -
100B ILE* 3.4 41.5 - - + -
103B GLY* 3.8 7.2 - - - -
104B GLU* 3.7 10.8 - - - -
107B ALA* 3.6 25.1 - - + -
108B LEU* 6.3 0.2 - - + -
281B LEU* 3.5 27.4 - - + -
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Residues in contact with ALA 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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62B GLU* 2.9 20.5 + - + +
63B ARG* 3.2 14.8 + - - +
65B PHE* 1.3 77.6 - - - +
67B LEU* 1.3 62.1 + - + +
69B ASP 3.8 2.2 - - - -
70B PRO* 2.9 36.8 - - + +
72B THR* 3.6 11.4 + - - +
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Residues in contact with LEU 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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15B GLU* 2.9 32.1 - - - +
18B LEU* 3.5 39.9 - - + +
19B ARG* 3.7 40.2 + - + +
22B LEU* 4.1 15.9 - - + +
63B ARG* 2.8 25.7 + - + +
64B VAL* 3.6 6.5 - - - +
66B ALA* 1.3 76.6 - - + +
68B ALA* 1.3 66.1 + - - +
69B ASP* 4.4 0.3 - - - -
70B PRO* 4.9 2.3 - - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.9 14.5 - - + +
26B LEU* 5.5 2.2 - - - -
64B VAL 3.0 13.0 + - - +
65B PHE 3.5 8.7 - - - +
67B LEU* 1.3 78.2 - - - +
69B ASP* 1.3 61.2 + - - +
70B PRO* 4.7 0.2 - - - -
99B GLY* 3.5 27.9 - - - +
102B ALA* 4.5 8.4 - - + +
103B GLY* 4.1 15.5 - - - +
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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 PHE 3.0 5.4 + - - +
66B ALA 3.1 2.7 - - - -
67B LEU 3.3 0.8 - - - -
68B ALA* 1.3 80.5 - - - +
70B PRO* 1.3 69.6 - - - +
71B ARG* 2.8 58.4 + - - -
72B THR* 2.8 32.6 + - + -
96B PRO* 3.6 15.4 - - - +
99B GLY* 4.0 18.5 + - - -
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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