Contacts of the helix formed by residues 51 - 67 (chain A) in PDB entry 1AX8
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 LEU 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A THR* 1.3 75.6 - - - +
52A SER* 1.3 61.4 + - - +
54A MET* 3.5 7.7 + - - +
55A ASP* 3.1 25.1 + - - +
87A LEU* 4.3 14.8 - - + +
90A LEU* 3.9 24.5 - - + -
91A ALA* 4.0 27.8 - - + +
94A LYS* 3.8 28.9 - - - +
98A LEU* 3.7 20.0 - - + +
140A LEU* 4.3 11.9 - - + -
144A PRO* 3.9 19.5 - - + -
145A GLY 3.1 15.2 + - - +
146A CYS* 3.6 3.3 + - - +
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 3.1 6.0 - - - -
51A LEU* 1.3 76.4 - - - +
53A LYS* 1.3 60.5 + - - +
55A ASP* 3.5 5.0 + - - +
56A GLN* 2.9 30.4 + - - +
97A HIS 3.8 1.6 + - - -
98A LEU* 3.3 10.6 - - - +
99A PRO* 3.1 32.7 - - - +
146A CYS* 2.9 24.5 + - - -
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Residues in contact with LYS 53 (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 HIS* 4.6 6.7 - - + -
48A ILE* 3.2 56.1 - - + +
49A LEU* 3.4 23.8 - - + +
50A THR* 3.3 23.5 + - - +
52A SER* 1.3 75.7 - - - +
54A MET* 1.3 61.9 + - - +
56A GLN* 3.8 6.2 - - - +
57A THR* 2.7 34.2 + - - -
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Residues in contact with MET 54 (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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48A ILE 4.1 13.0 - - - +
49A LEU 3.5 21.3 - - - +
50A THR 3.1 13.0 + - - +
51A LEU* 3.7 12.3 - - - +
53A LYS* 1.3 75.9 - - - +
55A ASP* 1.3 56.7 + - - +
57A THR* 3.2 5.9 + - - -
58A LEU* 3.0 31.9 + - - +
87A LEU* 3.9 17.3 - - + -
136A MET* 3.8 32.2 - - + +
139A GLN* 4.0 29.6 - - + +
140A LEU* 3.6 34.1 - - + -
144A PRO* 4.0 7.4 - - + -
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Residues in contact with ASP 55 (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 LEU 3.1 15.0 + - - +
52A SER* 3.7 6.6 - - - +
54A MET* 1.3 78.5 - - - +
56A GLN* 1.3 65.2 + - - +
58A LEU* 3.3 4.7 + - - +
59A ALA* 3.0 22.9 + - - +
84A ARG* 2.8 45.6 + - - +
87A LEU* 3.8 11.3 - - + +
88A HIS* 3.0 32.5 + - + -
98A LEU* 4.6 6.2 - - + +
99A PRO 4.3 9.0 - - - +
101A ALA* 4.2 6.2 - - - +
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Residues in contact with GLN 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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46A HIS* 4.4 17.9 - - + +
52A SER 2.9 21.3 + - - +
53A LYS* 3.9 5.6 - - - +
55A ASP* 1.3 74.7 + - - +
57A THR* 1.3 61.9 + - - +
59A ALA* 3.6 1.9 + - - +
60A VAL* 3.3 26.3 + - - +
101A ALA* 3.8 17.5 - - + +
102A SER* 3.0 53.4 + - - +
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Residues in contact with THR 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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45A LEU* 3.2 24.2 - - + +
46A HIS* 3.6 28.2 + - - -
47A PRO* 3.7 15.7 - - + +
53A LYS 2.7 22.6 + - - -
54A MET* 3.4 6.1 - - - -
56A GLN* 1.3 74.0 - - - +
58A LEU* 1.3 65.6 + - - +
59A ALA 3.1 0.2 - - - -
60A VAL* 3.0 16.0 + - - +
61A TYR* 3.0 36.5 + - + -
132A SER* 4.3 2.2 - - - +
136A MET* 4.6 3.6 - - + -
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Residues in contact with LEU 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 MET 3.0 16.7 + - - +
55A ASP 3.3 4.9 + - - +
57A THR* 1.3 75.2 - - - +
59A ALA* 1.3 57.0 + - - +
61A TYR* 3.2 8.4 + - + +
62A GLN* 2.9 34.5 + - - +
80A LEU* 4.2 17.4 - - + +
83A LEU* 3.8 31.9 - - + -
84A ARG* 3.8 22.4 - - + +
87A LEU* 3.5 29.6 - - + -
129A LEU* 4.7 9.6 - - + -
133A LEU* 4.5 8.1 - - + -
136A MET* 3.3 26.0 - - + -
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Residues in contact with ALA 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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55A ASP 3.0 17.7 + - - +
56A GLN* 3.7 8.5 - - - +
57A THR 3.1 0.2 - - - -
58A LEU* 1.3 78.3 - - - +
60A VAL* 1.3 59.7 + - - +
62A GLN* 3.4 7.5 + - - +
63A GLN* 3.2 28.0 + - - +
84A ARG* 3.6 31.4 - - - +
101A ALA* 3.8 13.7 - - + -
102A SER 5.1 2.5 - - - +
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Residues in contact with VAL 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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45A LEU* 3.8 26.9 - - + -
46A HIS* 5.4 7.0 - - + +
56A GLN* 3.3 27.1 + - + +
57A THR* 3.0 11.7 + - - +
59A ALA* 1.3 73.8 - - - +
61A TYR* 1.3 67.2 + - - +
63A GLN* 3.4 13.1 + - - +
64A ILE* 3.2 23.8 + - + +
102A SER 5.1 3.1 - - - +
104A LEU* 4.0 27.8 - - + -
110A LEU* 4.6 5.4 - - + -
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Residues in contact with TYR 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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45A LEU* 2.9 44.0 + - + -
57A THR* 3.0 39.8 + - + -
58A LEU* 3.2 9.8 + - + +
60A VAL* 1.3 74.0 - - - +
62A GLN* 1.3 59.6 + - - +
64A ILE* 3.0 13.8 + - + +
65A LEU* 2.8 36.1 + - + +
80A LEU* 3.8 14.8 - - + -
125A ALA* 4.0 10.5 - - + -
128A ARG* 3.3 14.9 - - + +
129A LEU* 3.5 41.3 - - + -
132A SER* 2.7 36.2 + - - -
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Residues in contact with GLN 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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58A LEU 2.9 17.2 + - - +
59A ALA* 3.7 5.9 - - - +
60A VAL 3.3 0.2 - - - -
61A TYR* 1.3 77.1 - - - +
63A GLN* 1.3 59.9 + - - +
65A LEU* 3.4 4.8 + - - +
66A THR* 2.8 31.9 + - - +
77A SER* 3.5 16.7 + - - +
80A LEU* 3.4 20.6 - - + -
81A GLU* 3.1 53.5 + - - +
84A ARG* 3.3 34.3 + - - -
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Residues in contact with GLN 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 ALA 3.2 15.3 + - - +
60A VAL* 3.6 11.1 - - - +
61A TYR 3.2 0.4 - - - -
62A GLN* 1.3 77.8 - - + +
64A ILE* 1.3 63.6 + - - +
66A THR* 3.6 11.6 + - - -
67A SER* 3.7 4.2 + - - -
102A SER 4.5 2.3 - - - +
103A GLY* 3.6 9.9 - - - -
104A LEU* 2.9 63.6 + - + +
107A LEU* 3.5 28.1 - - + +
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Residues in contact with ILE 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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45A LEU* 3.6 30.3 - - + -
60A VAL* 3.3 18.6 - - + +
61A TYR* 3.0 17.6 + - + +
63A GLN* 1.3 77.7 - - + +
65A LEU* 1.3 61.7 + - + +
67A SER* 2.8 31.0 + - - +
68A MET* 3.4 26.9 - - + +
104A LEU* 5.6 0.2 - - + -
107A LEU* 4.1 13.0 - - + -
110A LEU* 4.3 13.0 - - + -
114A LEU* 4.1 28.0 - - + -
125A ALA* 3.9 15.9 - - + -
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Residues in contact with LEU 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 TYR* 2.8 26.0 + - + +
62A GLN 3.9 1.1 - - - +
64A ILE* 1.3 78.8 - - + +
66A THR* 1.3 61.6 + - - +
67A SER 3.1 0.4 - - - -
68A MET* 3.3 30.4 + - - -
69A PRO* 3.8 1.7 - - - +
73A VAL* 3.1 32.8 - - + +
76A ILE* 3.7 30.3 - - + -
77A SER* 3.9 24.6 - - - +
80A LEU* 4.0 15.9 - - + -
125A ALA* 5.1 4.3 - - + -
126A LEU* 4.0 21.5 - - + -
129A LEU* 4.3 6.3 - - + -
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Residues in contact with THR 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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62A GLN* 2.8 22.9 + - - +
63A GLN* 3.9 8.2 - - - -
64A ILE 3.1 0.6 - - - -
65A LEU* 1.3 77.7 - - - +
67A SER* 1.3 59.8 + - - +
68A MET 3.3 1.3 + - - -
69A PRO* 3.7 11.7 - - - +
77A SER* 4.2 8.1 + - - -
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Residues in contact with SER 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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63A GLN 3.7 2.1 + - - -
64A ILE* 2.8 17.9 + - - +
66A THR* 1.3 79.9 - - - +
68A MET* 1.3 65.7 + - - +
69A PRO* 3.5 5.6 - - - +
107A LEU* 3.4 27.6 - - - +
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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