Contacts of the helix formed by residues 52 - 67 (chain A) in PDB entry 1YZ3
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 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP 5.4 2.9 - - - -
49A ASN* 3.2 23.3 + - - -
50A PRO 4.2 0.2 - - - +
51A ASN* 1.3 83.3 - - - +
53A VAL* 1.3 64.6 + - - -
54A GLY 3.4 2.2 - - - -
55A PRO* 3.5 6.2 - - - +
56A TRP* 3.3 21.3 + - - +
256A TYR* 3.3 3.6 - - - -
259A PRO* 5.6 0.2 - - - -
261A HIS* 5.4 3.1 - - - -
262A LEU* 4.1 10.3 - - - -
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Residues in contact with VAL 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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39A ASN 5.7 0.2 - - - +
44A ARG* 4.2 21.5 + - + +
52A GLY* 1.3 70.6 - - - -
54A GLY* 1.3 71.1 + - - +
56A TRP* 4.2 2.5 - - + -
57A LYS* 2.9 36.5 + - + +
256A TYR* 3.2 27.5 + - + -
258A MET* 3.8 16.2 - - + -
262A LEU* 3.6 15.6 - - + +
272A VAL* 4.1 11.7 - - + -
3001A SKA 3.4 33.0 - - + -
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Residues in contact with GLY 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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44A ARG 4.1 7.2 + - - -
47A LEU* 3.8 17.7 - - - -
53A VAL* 1.3 87.0 - - - +
55A PRO* 1.3 69.7 - - - +
57A LYS* 3.3 9.3 + - - +
58A LEU* 3.2 26.4 + - - +
126A TYR* 4.5 10.7 - - - -
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Residues in contact with PRO 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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44A ARG 5.5 0.2 - - - +
46A ASP 4.5 2.5 - - - +
47A LEU* 3.7 33.2 - - + +
49A ASN 3.1 22.2 - - - +
50A PRO* 3.8 18.8 - - + +
52A GLY* 3.5 12.1 - - - +
54A GLY* 1.3 88.9 - - - +
56A TRP* 1.3 61.7 + - - +
58A LEU* 3.2 3.3 + - - +
59A ARG* 2.9 34.8 + - - +
129A HIS* 3.6 26.7 - - + +
133A ILE* 4.3 0.3 - - - +
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Residues in contact with TRP 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 GLY 3.3 16.8 + - - +
53A VAL* 3.6 4.3 - - + +
54A GLY 3.3 0.2 - - - -
55A PRO* 1.3 79.3 - - - +
57A LYS* 1.3 88.2 + - + +
59A ARG* 3.3 19.3 + - - +
60A CYS* 3.1 42.9 + - + -
214A ILE* 5.6 1.3 - - + -
254A ARG* 3.8 19.8 - - + +
255A THR 3.8 5.5 + - - -
256A TYR* 3.5 48.8 - + + +
272A VAL* 3.6 37.9 - - + -
273A PHE 4.4 0.7 - - - -
274A PHE* 3.6 28.3 - + + -
237B GLU* 3.5 34.4 + - - +
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Residues in contact with LYS 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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39A ASN 5.6 0.2 + - - -
40A TYR* 3.4 26.6 + - - -
53A VAL* 2.9 27.1 + - + +
54A GLY* 3.7 8.3 - - - +
56A TRP* 1.3 97.3 - - + +
58A LEU* 1.3 65.1 + - + +
60A CYS* 3.2 7.6 + - - +
61A LEU* 3.1 26.7 + - - +
85A TYR* 3.3 34.4 + - + +
126A TYR* 5.7 1.8 - - - -
182A PHE* 3.6 23.0 - - + -
214A ILE* 4.1 18.7 - - + +
272A VAL* 4.7 0.7 - - + -
3001A SKA 3.5 24.2 - - - +
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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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47A LEU* 4.4 3.1 - - + -
54A GLY 3.2 12.1 + - - +
55A PRO 3.2 7.0 + - - +
57A LYS* 1.3 73.9 - - + +
59A ARG* 1.3 59.6 + - - +
61A LEU* 3.4 7.9 + - + +
62A ALA* 2.8 32.4 + - - +
85A TYR* 4.0 37.2 - - + +
88A LEU* 4.6 11.2 - - + -
89A SER* 4.5 3.2 + - - +
126A TYR* 3.8 25.6 - - + +
129A HIS* 3.6 34.5 - - + -
130A ALA* 4.3 9.0 - - + +
133A ILE* 3.6 13.7 - - + -
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Residues in contact with ARG 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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50A PRO* 3.1 34.7 + - - +
51A ASN* 5.1 3.6 + - - +
55A PRO* 2.9 23.3 + - - +
56A TRP* 3.6 28.3 - - - +
58A LEU* 1.3 76.0 - - - +
60A CYS* 1.3 59.2 + - - +
62A ALA* 4.4 2.7 - - - -
63A GLN* 2.8 58.0 + - - +
129A HIS* 5.2 1.8 + - - -
133A ILE* 3.8 22.9 - - + +
254A ARG* 5.3 1.8 - - - +
256A TYR* 6.0 0.2 - - - -
237B GLU* 3.3 37.7 + - - +
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Residues in contact with CYS 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 TRP* 3.1 52.4 + - + -
57A LYS* 3.2 10.7 + - - +
59A ARG* 1.3 77.9 - - - +
61A LEU* 1.3 61.0 + - - +
63A GLN* 4.2 1.2 - - - +
64A THR* 3.0 27.7 + - - -
254A ARG* 4.1 25.4 + - - +
274A PHE* 3.5 39.3 - - + -
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Residues in contact with LEU 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 LYS 3.1 15.5 + - - +
58A LEU* 3.9 10.8 - - + +
60A CYS* 1.3 77.2 - - - +
62A ALA* 1.3 62.5 + - - +
64A THR* 3.3 3.5 + - - -
65A PHE* 3.0 39.7 + - + -
85A TYR* 4.4 9.6 - - + +
86A GLN* 3.8 37.2 - - + +
89A SER* 4.3 8.7 - - - +
179A VAL* 5.2 4.9 - - + -
212A LEU* 4.1 24.2 - - + -
214A ILE* 4.1 21.8 - - + -
274A PHE* 3.9 18.8 - - + -
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Residues in contact with ALA 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 2.8 22.8 + - - +
59A ARG 3.9 0.9 - - - +
61A LEU* 1.3 72.7 - - - +
63A GLN* 1.3 56.2 + - - +
65A PHE* 3.7 2.3 + - - +
66A ALA* 3.0 29.2 + - - +
89A SER* 3.3 24.8 + - - +
130A ALA* 6.2 0.7 - - - -
133A ILE* 3.8 27.6 - - + -
134A GLU* 4.3 14.6 - - + +
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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 ARG* 2.8 49.1 + - - +
62A ALA* 1.3 71.0 - - + +
64A THR* 1.3 67.8 + - - +
66A ALA* 3.1 17.3 + - - +
67A THR* 3.3 13.8 + - - +
133A ILE* 5.6 4.1 - - + +
254A ARG* 2.8 44.1 + - - +
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Residues in contact with THR 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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60A CYS 3.0 17.6 + - - -
61A LEU 3.3 5.3 + - - -
63A GLN* 1.3 76.3 - - - +
65A PHE* 1.3 58.8 + - - +
67A THR* 2.6 37.5 + - - -
70A VAL* 4.0 14.2 - - + +
212A LEU* 3.5 30.1 - - + -
252A ASP* 5.0 0.9 + - - -
254A ARG* 5.0 3.0 + - - +
274A PHE* 3.1 21.2 - - - -
276A TRP* 3.8 26.7 - - + +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 3.0 37.2 + - + +
62A ALA 4.2 2.5 - - - +
64A THR* 1.3 78.5 - - - +
66A ALA* 1.3 61.5 + - - +
67A THR 3.2 0.4 - - - -
68A GLY* 3.4 10.0 + - - +
70A VAL* 3.8 31.6 - - + +
75A LEU* 4.7 1.6 - - + -
86A GLN 5.5 0.9 - - - -
89A SER* 4.2 7.0 - - - +
90A ALA* 3.2 41.7 - - + -
93A HIS* 3.1 43.0 + + + -
94A PHE* 3.7 24.7 - + - -
179A VAL* 4.6 5.2 - - + -
212A LEU* 3.1 32.1 - - + -
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Residues in contact with ALA 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 ALA 3.0 19.7 + - - +
63A GLN* 3.3 12.6 - - - +
64A THR 3.0 0.6 + - - -
65A PHE* 1.3 74.1 - - - +
67A THR* 1.3 62.7 + - - +
68A GLY* 3.1 3.9 + - - -
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Residues in contact with THR 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 3.4 15.9 - - - +
64A THR* 2.6 19.0 + - - +
66A ALA* 1.3 79.2 - - - +
68A GLY* 1.3 61.6 + - - +
69A GLU* 3.3 31.8 + - - +
70A VAL 4.9 0.2 + - - -
276A TRP* 3.9 17.7 - - + -
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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