Contacts of the helix formed by residues 50 - 63 (chain A) in PDB entry 1Z29
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 5.0 2.7 - - - -
48A LYS 3.6 0.2 - - - -
49A SER* 1.3 78.7 - - - +
51A THR* 1.3 60.8 + - - +
52A THR 3.4 2.2 - - - -
53A TRP* 3.2 15.4 + - - +
54A VAL* 2.9 34.5 + - - +
128A VAL* 4.7 5.6 - - - +
193A TYR* 4.0 14.9 - - - -
196A MET* 5.2 0.7 - - - +
2001A A3P 3.2 12.0 + - - -
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Residues in contact with THR 51 (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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43A ILE* 4.2 11.7 - - + -
45A THR* 2.6 35.3 + - - +
46A TYR 4.4 0.3 + - - -
49A SER 3.7 0.6 - - - -
50A GLY* 1.3 77.2 + - - +
52A THR* 1.3 53.2 + - - +
54A VAL* 3.5 4.5 - - - +
55A SER* 2.6 38.4 + - - +
106A LYS* 3.7 35.9 - - + -
107A THR 5.2 1.6 - - - +
108A HIS* 3.1 15.4 - - + -
2001A A3P 2.6 25.2 + - - -
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Residues in contact with THR 52 (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 THR* 1.3 74.4 - - - +
53A TRP* 1.3 62.8 + - - +
55A SER* 3.6 6.5 - - - -
56A GLN* 3.1 23.0 + - - +
75A ILE* 4.4 14.6 - - + +
232A MET* 3.6 12.7 - - + +
238A THR* 3.7 22.9 - - - +
240A TYR* 3.7 18.6 + - + -
255A PHE* 3.2 19.7 - - - -
256A MET* 4.1 7.9 - - + -
2001A A3P 2.6 29.0 + - - -
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Residues in contact with TRP 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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50A GLY* 3.2 12.0 + - - +
51A THR 3.2 0.4 - - - -
52A THR* 1.3 81.4 - - - +
54A VAL* 1.3 62.8 + - - +
56A GLN* 3.3 2.6 + - - +
57A ILE* 3.2 36.9 + - + +
193A TYR* 3.8 32.5 - + - -
196A MET* 3.3 61.9 - - + -
197A LYS* 3.6 10.3 - - + -
200A PRO* 4.8 10.5 - - + -
227A THR* 3.0 20.9 + - - -
228A SER* 5.8 2.2 - - - -
232A MET* 4.0 10.5 - - - -
2001A A3P 3.3 56.3 + + + +
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Residues in contact with VAL 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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43A ILE* 3.5 31.9 - - + -
50A GLY 2.9 16.4 + - - +
51A THR* 3.5 7.4 - - - +
53A TRP* 1.3 75.2 - - - +
55A SER* 1.3 60.1 + - - +
57A ILE* 3.4 5.1 + - - +
58A LEU* 2.9 31.7 + - + +
126A VAL* 3.9 25.8 - - + -
128A VAL* 4.0 20.0 - - + -
191A LEU* 4.5 1.3 - - + -
196A MET* 4.2 13.2 - - + +
207A ILE* 3.9 21.8 - - + -
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Residues in contact with SER 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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43A ILE* 3.4 26.7 - - - +
51A THR* 2.6 30.5 + - - +
52A THR* 3.6 6.9 - - - -
53A TRP 3.1 0.2 - - - -
54A VAL* 1.3 74.9 - - - +
56A GLN* 1.3 60.5 + - - +
58A LEU* 3.4 1.6 + - - +
59A ASP* 2.9 31.0 + - - +
75A ILE* 3.9 20.0 - - - +
79A VAL* 4.2 16.0 - - - +
106A LYS* 5.0 4.3 - - - +
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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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52A THR 3.1 16.8 + - - +
53A TRP 3.3 2.7 + - - +
55A SER* 1.3 75.8 - - - +
57A ILE* 1.3 64.2 + - - +
59A ASP* 3.3 7.2 + - - +
60A MET* 3.0 39.3 + - - +
75A ILE* 3.3 15.0 - - + +
78A ARG* 6.0 1.0 - - - -
226A HIS 5.4 2.9 + - - +
227A THR* 4.1 13.2 - - + -
232A MET* 3.6 29.5 - - + +
235A ASN* 4.1 9.5 + - - -
238A THR* 3.2 26.6 - - + +
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Residues in contact with ILE 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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53A TRP* 3.2 32.8 + - + +
54A VAL* 3.6 8.1 - - - +
55A SER 3.2 0.2 - - - -
56A GLN* 1.3 79.7 - - - +
58A LEU* 1.3 62.7 + - - +
60A MET 3.2 0.3 + - - -
61A ILE* 3.0 35.6 + - + +
196A MET* 4.0 17.5 - - + -
200A PRO* 6.2 1.1 - - + -
204A ILE* 3.7 31.9 - - + -
207A ILE* 4.0 15.7 - - + -
223A MET* 3.5 20.7 - - + +
227A THR* 3.8 22.4 - - + +
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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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41A LEU* 3.5 22.0 - - + -
43A ILE* 3.4 30.5 - - + -
54A VAL* 2.9 21.9 + - + +
55A SER 3.9 3.1 - - - +
57A ILE* 1.3 77.5 - - - +
59A ASP* 1.3 57.5 + - - +
61A ILE* 3.4 5.9 + - + +
62A TYR* 2.9 56.3 + - + -
104A LEU* 3.8 11.4 - - + -
126A VAL* 4.2 13.9 - - + -
207A ILE* 3.5 29.8 - - + -
211A VAL* 4.2 11.2 - - + -
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Residues in contact with ASP 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 SER 2.9 17.0 + - - +
56A GLN* 3.7 11.8 - - - +
58A LEU* 1.3 74.6 - - - +
60A MET* 1.3 67.0 + - + +
62A TYR* 3.3 2.5 + - - +
63A GLN* 2.9 41.6 + - - +
75A ILE* 4.9 3.5 - - + +
78A ARG* 2.7 54.3 + - - +
79A VAL* 4.7 5.3 - - + +
104A LEU* 3.6 19.2 - - + +
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Residues in contact with MET 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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56A GLN* 3.0 31.9 + - - +
57A ILE 3.6 6.7 - - - +
59A ASP* 1.3 76.5 - - + +
61A ILE* 1.3 59.0 + - - +
63A GLN* 2.8 13.2 + - - +
64A GLY 3.2 0.2 + - - -
65A GLY* 2.7 48.4 + - - +
222A LEU 4.8 0.7 - - - +
223A MET* 3.9 32.3 - - + -
226A HIS* 3.9 31.0 - - + +
227A THR* 3.3 29.4 - - - -
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Residues in contact with ILE 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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57A ILE* 3.0 29.0 + - + +
58A LEU* 3.5 9.0 - - + +
60A MET* 1.3 75.6 - - - +
62A TYR* 1.3 64.8 + - + +
64A GLY* 3.1 19.4 + - - -
204A ILE* 4.5 2.0 - - + -
207A ILE* 3.8 30.5 - - + -
208A LEU* 3.8 35.9 - - + +
211A VAL* 4.3 5.8 - - + -
213A ARG* 3.6 31.3 + - + -
215A LEU* 4.5 12.5 - - + +
223A MET* 3.6 16.1 - - + +
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Residues in contact with TYR 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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39A ASP 5.1 3.3 + - - -
41A LEU* 3.7 23.1 - - + +
58A LEU* 2.9 42.7 + - + +
59A ASP* 3.8 5.6 - - - +
60A MET 3.2 0.2 - - - -
61A ILE* 1.3 85.1 - - + +
63A GLN* 1.3 69.6 + - - +
64A GLY 3.4 1.1 - - - -
102A PRO* 4.0 31.6 - - + -
103A ARG 5.6 0.4 - - - -
104A LEU* 3.5 36.1 - - + -
211A VAL* 4.1 12.5 + - + +
213A ARG* 3.6 44.5 + - - +
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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 ASP* 2.9 25.9 - - - +
60A MET* 2.8 11.1 + - - +
62A TYR* 1.3 89.0 + - - +
64A GLY* 1.3 61.6 + - - +
65A GLY 3.2 7.1 + - - +
78A ARG* 3.8 27.0 + - - +
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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