Contacts of the helix formed by residues 61 - 80 (chain A) in PDB entry 4YET
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 THR 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLN* 1.3 82.1 + - - +
62A GLY* 1.3 70.8 + - - +
63A ALA 3.6 1.0 + - - -
64A VAL* 3.8 7.3 + - - +
65A PHE* 3.4 15.6 + - + -
147A LYS* 4.6 9.2 - - - +
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Residues in contact with GLY 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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61A THR* 1.3 78.3 + - - +
63A ALA* 1.3 58.8 + - - -
65A PHE* 3.2 4.1 + - - +
66A ASN* 2.9 38.2 + - - +
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 5.7 3.6 - - - -
42A LEU* 3.8 22.0 - - + -
61A THR 3.6 0.4 + - - -
62A GLY* 1.3 69.0 - - - -
64A VAL* 1.3 66.6 - - + +
66A ASN* 4.4 8.9 - - - +
67A ASN* 2.8 37.1 + - - +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.9 16.4 - - + +
42A LEU* 4.1 28.9 - - + +
43A ILE* 4.4 3.1 - - + -
48A MET* 4.2 27.1 - - + -
56A LEU* 4.2 12.3 - - + -
60A GLN* 3.8 27.8 - - + +
61A THR 3.8 6.7 + - - +
62A GLY 3.3 0.6 - - - -
63A ALA* 1.3 76.6 - - + +
65A PHE* 1.3 64.0 + - - +
68A ALA* 3.0 23.0 + - - +
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Residues in contact with PHE 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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56A LEU 4.7 2.9 - - - -
57A ILE* 3.3 44.6 - - + -
60A GLN* 3.4 23.7 - - - +
61A THR* 3.4 12.0 + - - -
62A GLY 3.2 9.2 + - - +
64A VAL* 1.3 79.6 - - - +
66A ASN* 1.3 75.2 + - - +
68A ALA* 3.2 3.7 + - - -
69A ALA* 2.8 43.6 + - + +
142A ALA* 3.9 21.5 - - + -
143A GLY* 4.5 3.6 - - - -
144A SER* 4.3 13.5 - - - -
147A LYS* 4.0 17.3 - - + -
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY* 2.9 24.6 + - - +
63A ALA* 3.3 8.8 + - - +
65A PHE* 1.3 90.2 - - - +
67A ASN* 1.3 62.3 + - - +
70A GLN* 3.0 35.4 + - - +
141A ASP* 5.8 0.3 - - - +
142A ALA* 3.6 13.5 + - - +
119B PHE* 3.5 49.3 - - + +
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Residues in contact with ASN 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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35A TYR* 3.3 39.3 - - - +
38A LYS* 3.4 39.5 - - - +
39A LEU* 4.0 11.9 - - + +
42A LEU* 3.8 4.0 - - - +
63A ALA* 2.8 34.8 + - - +
64A VAL 4.2 0.9 - - - +
66A ASN* 1.3 77.4 - - - +
68A ALA* 1.3 67.1 + - - +
70A GLN* 3.3 1.6 + - - +
71A ILE* 2.9 30.7 + - - +
119B PHE* 6.0 1.6 - - - -
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Residues in contact with ALA 68 (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 LEU* 4.0 20.9 - - + +
53A ILE* 3.8 9.4 - - + +
56A LEU* 3.9 27.6 - - + -
57A ILE* 3.9 12.6 - - + +
64A VAL 3.0 18.8 + - - +
65A PHE* 3.8 2.7 - - - +
67A ASN* 1.3 76.1 - - - +
69A ALA* 1.3 62.3 + - - +
71A ILE* 3.2 6.8 + - - +
72A TRP* 3.1 21.3 + - - +
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Residues in contact with ALA 69 (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* 3.8 15.1 - - + +
65A PHE* 2.8 38.5 + - + +
68A ALA* 1.3 73.5 - - - +
70A GLN* 1.3 58.6 + - - +
72A TRP* 3.2 1.9 + - - +
73A ASN* 2.7 36.8 + - - +
142A ALA* 3.2 28.3 - - + +
144A SER* 4.6 4.9 - - - -
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Residues in contact with GLN 70 (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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35A TYR* 3.3 51.0 + - + -
66A ASN 3.0 23.3 + - - +
67A ASN 3.9 0.2 - - - +
69A ALA* 1.3 75.6 - - - +
71A ILE* 1.3 63.3 + - - +
73A ASN* 3.4 2.4 + - - -
74A HIS* 2.7 46.8 + - - +
123A TRP* 3.1 25.6 + - - -
141A ASP 4.2 0.2 - - - -
142A ALA* 3.4 22.7 - - + -
160A TRP* 3.5 26.2 - - - +
119B PHE* 3.9 3.8 - - + -
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Residues in contact with ILE 71 (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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3A PHE* 5.3 2.7 - - + -
32A HIS* 3.1 30.3 + - + +
35A TYR* 3.6 29.2 - - + +
36A VAL* 3.7 24.5 - - + +
39A LEU* 3.6 29.6 - - + -
53A ILE* 4.1 9.0 - - + -
67A ASN 2.9 20.9 + - - +
68A ALA 3.5 6.1 - - - +
69A ALA 3.2 0.2 - - - -
70A GLN* 1.3 77.4 - - - +
72A TRP* 1.3 63.2 + - - +
75A THR* 3.1 14.2 + - - -
198A TRP* 3.6 32.5 - - + +
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Residues in contact with TRP 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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53A ILE* 3.7 13.7 - - + +
54A GLU* 2.9 32.8 + - + +
57A ILE* 3.6 25.6 - - + -
68A ALA 3.1 3.9 + - - +
69A ALA 3.6 2.7 - - - +
71A ILE* 1.3 78.7 - - - +
73A ASN* 1.3 76.3 + - - +
75A THR* 3.2 3.8 + - - -
76A PHE* 2.9 53.5 + + + +
125A TRP* 4.1 15.5 - + - -
144A SER* 5.4 1.3 - - - -
145A PRO* 5.1 0.7 - - + -
146A LEU* 3.8 24.7 - - + -
153A PRO* 3.8 21.3 - - + -
196A PHE* 3.7 30.1 - + + -
198A TRP* 3.5 28.3 - + + +
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Residues in contact with ASN 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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57A ILE* 5.9 0.2 - - - +
69A ALA 2.7 27.2 + - - +
70A GLN* 3.4 13.5 + - - +
72A TRP* 1.3 84.5 - - - +
74A HIS* 1.3 56.4 + - - +
76A PHE* 3.3 3.3 + - - +
77A TYR* 2.8 28.4 + - - +
123A TRP* 3.4 33.2 - - + +
125A TRP* 3.3 27.0 - - + -
142A ALA 3.3 23.4 + - - -
143A GLY 3.5 10.5 + - - +
144A SER* 4.6 8.5 - - - -
145A PRO* 4.6 0.2 - - - +
156A CYS* 3.8 1.6 - - - -
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Residues in contact with HIS 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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27A HIS* 3.2 20.9 + + - -
31A HIS* 5.2 0.4 - - - +
32A HIS* 3.4 29.6 - + + +
35A TYR* 3.6 17.5 - + - -
70A GLN* 2.7 56.6 + - - +
73A ASN* 1.3 73.2 - - - +
75A THR* 1.3 66.8 + - - +
77A TYR* 3.1 7.6 + + - +
78A TRP* 2.9 38.1 + + - +
123A TRP* 3.6 10.4 - + - -
158A ASP* 3.5 3.5 + - - -
162A HIS* 3.8 1.4 + - - -
300A FE 2.2 31.1 - - - -
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Residues in contact with THR 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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6A PRO* 3.8 20.6 - - + +
32A HIS* 3.2 20.2 + - - -
71A ILE 3.1 6.6 + - - -
72A TRP 3.7 0.4 - - - -
74A HIS* 1.3 75.8 - - - +
76A PHE* 1.3 62.4 + - - +
78A TRP* 3.4 7.0 + - - +
79A ASN* 2.9 37.2 + - - +
196A PHE* 3.8 17.9 - - + -
198A TRP* 3.0 40.8 + - + +
199A SER 5.1 1.8 - - - +
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Residues in contact with PHE 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 TRP* 2.9 37.8 + + + +
73A ASN* 3.5 8.7 - - - +
75A THR* 1.3 78.2 - - - +
77A TYR* 1.3 56.8 + - - +
79A ASN* 3.2 2.6 + - - -
80A SER* 2.9 36.8 + - - -
125A TRP* 3.7 13.5 - + + -
153A PRO* 3.3 41.7 - - + -
154A LEU 3.5 1.3 - - - -
155A LEU* 3.5 28.9 - - - -
156A CYS* 3.8 5.8 - - - -
187A PHE* 3.6 25.5 - + - -
191A ASN* 3.4 16.6 - - - -
196A PHE* 3.7 23.5 - + + -
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Residues in contact with TYR 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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19A ILE* 3.8 16.8 - - - +
27A HIS* 3.6 21.4 + + - -
73A ASN 2.8 14.2 + - - +
74A HIS* 3.3 9.9 - + - +
76A PHE* 1.3 74.1 - - - +
78A TRP* 1.3 105.4 + + - +
80A SER* 3.1 16.1 + - - -
81A MET* 3.5 26.1 + - + +
123A TRP* 3.9 4.9 - - + -
156A CYS* 3.5 23.0 - - - -
157A CYS* 4.1 4.3 - - - -
158A ASP* 3.5 35.0 - - + -
163A ALA* 4.2 5.7 + - - +
175A TYR* 2.7 27.6 + - - -
179A TRP* 4.2 3.8 - - - -
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Residues in contact with TRP 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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6A PRO 5.8 0.7 - - - -
7A ALA 6.1 0.4 - - - -
8A LEU* 3.5 16.4 - - + -
9A PRO* 3.8 18.2 - - + -
10A TYR* 2.8 34.5 + - - +
19A ILE* 5.8 0.4 - - + -
24A LEU* 3.5 26.0 - - + -
27A HIS* 3.5 40.8 - + + -
28A TYR* 3.5 33.0 - + + -
32A HIS* 2.9 30.5 + + - -
74A HIS* 2.9 33.7 + + - -
75A THR* 3.4 7.4 + - - +
77A TYR* 1.3 93.1 - + - +
79A ASN* 1.3 58.1 + - - +
81A MET* 3.1 31.2 + - + +
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Residues in contact with ASN 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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9A PRO* 3.8 25.0 - - - +
75A THR* 2.9 30.3 + - - +
76A PHE 3.7 2.5 - - - +
77A TYR 3.2 0.6 - - - -
78A TRP* 1.3 73.6 - - - +
80A SER* 1.3 58.1 + - - +
81A MET 3.1 6.7 - - - -
184A ASN* 3.3 14.4 + - - +
187A PHE* 3.2 55.3 - - + +
196A PHE* 4.4 8.3 - - - -
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Residues in contact with SER 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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76A PHE* 2.9 20.1 + - - -
77A TYR 3.1 10.7 + - - -
79A ASN* 1.3 75.9 - - - +
81A MET* 1.3 59.0 + - - +
155A LEU* 3.4 20.6 - - - +
156A CYS 3.1 39.0 + - - -
179A TRP* 4.6 4.1 - - - -
183A VAL* 3.6 6.9 - - - +
184A ASN* 2.8 22.2 + - - -
187A PHE* 3.8 10.3 - - - -
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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
------------------------------------------------------------
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