Contacts of the helix formed by residues 71 - 81 (chain A) in PDB entry 1X7O
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 4.8 0.9 - - - +
69A GLU* 3.9 1.2 + - - +
70A LEU* 1.3 77.5 - - - +
72A LYS* 1.3 64.7 + - - +
73A TRP* 3.2 9.2 + - - +
74A ALA 3.3 12.1 + - - -
75A ARG* 3.1 20.4 + - - +
105A GLU* 2.7 27.2 + - - -
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Residues in contact with LYS 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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71A SER* 1.3 75.5 - - - +
73A TRP* 1.3 61.4 + - - +
75A ARG* 3.7 7.6 + - - +
76A GLU* 3.1 25.5 + - - +
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Residues in contact with TRP 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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46A VAL* 3.3 35.1 - - + +
47A ARG* 3.9 35.2 - - + -
50A SER* 2.9 32.3 + - - -
71A SER* 3.1 9.0 + - - +
72A LYS* 1.3 77.2 - - - +
74A ALA* 1.3 66.3 + - - +
76A GLU* 3.0 10.4 + - + +
77A LEU* 2.9 25.9 + - + +
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Residues in contact with ALA 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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46A VAL* 4.0 8.8 - - + +
70A LEU* 4.1 11.9 - - + -
71A SER* 3.3 19.1 + - - +
73A TRP* 1.3 77.9 - - - +
75A ARG* 1.3 62.1 + - - +
77A LEU* 3.2 7.0 + - - +
78A LEU* 3.0 29.1 + - + +
105A GLU* 3.7 22.0 - - + +
106A VAL* 3.8 20.2 - - + -
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Residues in contact with ARG 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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70A LEU* 3.8 37.7 - - + +
71A SER 3.1 18.0 + - - +
72A LYS* 3.7 7.9 - - - +
74A ALA* 1.3 76.1 - - - +
76A GLU* 1.3 63.7 + - - +
78A LEU* 3.2 13.0 + - - +
79A ARG* 3.2 30.6 + - + +
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Residues in contact with GLU 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 LYS 3.1 11.9 + - - +
73A TRP* 3.0 15.7 + - + +
75A ARG* 1.3 77.3 - - - +
77A LEU* 1.3 65.5 + - - +
79A ARG* 2.9 38.5 + - - +
80A THR* 3.1 32.7 + - + +
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Residues in contact with LEU 77 (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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46A VAL* 3.9 44.2 - - + +
49A ILE* 4.1 27.8 - - + -
50A SER* 3.7 22.4 - - - +
53A VAL* 4.9 2.9 - - + -
62A LEU* 4.7 7.9 - - + -
73A TRP* 2.9 16.2 + - + +
74A ALA* 3.6 8.5 - - - +
76A GLU* 1.3 74.0 - - - +
78A LEU* 1.3 60.2 + - + +
80A THR* 3.9 5.8 - - + -
81A VAL* 2.9 55.6 + - + +
106A VAL* 5.0 6.7 - - + -
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Residues in contact with LEU 78 (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 LEU* 3.8 26.5 - - + -
64A TYR* 3.8 52.0 - - + -
70A LEU* 4.1 17.5 - - + -
74A ALA* 3.0 23.1 + - + +
75A ARG* 3.7 12.6 - - - +
76A GLU 3.2 0.4 - - - -
77A LEU* 1.3 79.1 - - + +
79A ARG* 1.3 59.8 + - + +
80A THR 3.8 0.2 + - - -
81A VAL 4.3 0.3 - - - +
85A GLN* 2.6 43.5 + - + +
106A VAL* 5.3 4.3 - - + -
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Residues in contact with ARG 79 (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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75A ARG* 3.2 21.4 + - + +
76A GLU* 2.9 34.7 + - - +
77A LEU 3.3 0.2 - - - -
78A LEU* 1.3 77.2 - - - +
80A THR* 1.3 67.4 + - - +
81A VAL 5.5 0.4 - - - -
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Residues in contact with THR 80 (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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53A VAL* 6.0 2.2 - - + -
76A GLU* 3.1 26.4 + - + +
77A LEU* 3.6 10.1 - - + +
79A ARG* 1.3 92.0 + - - +
81A VAL* 1.3 74.1 + - + +
82A ARG* 3.4 15.8 + - - +
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Residues in contact with VAL 81 (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 ILE* 5.7 0.2 - - + -
53A VAL* 4.0 30.7 - - + -
59A VAL* 4.5 11.4 - - + -
62A LEU* 4.0 12.6 - - + -
77A LEU* 2.9 40.4 + - + +
78A LEU 4.3 0.2 - - - +
79A ARG 5.5 0.4 - - - -
80A THR* 1.3 86.2 - - + +
82A ARG* 1.3 58.8 + - - +
83A THR* 3.1 26.9 + - + +
85A GLN* 3.0 25.1 + - - -
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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