Contacts of the helix formed by residues 68 - 80 (chain A) in PDB entry 4UT2
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 GLN 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.3 18.4 + - + +
66A HIS* 3.0 8.3 + - - +
67A GLY* 1.3 73.7 - - - +
69A TYR* 1.3 64.6 + - - +
70A TYR 3.3 2.5 - - - -
71A ASP* 2.8 46.3 + - + +
72A LEU 3.1 9.4 + - - -
97A GLY* 4.7 6.7 - - - -
103A THR* 4.0 1.7 + - - -
269A ALA* 3.6 19.7 - - - +
270A PRO 3.1 19.5 + - - -
271A ASN 4.5 2.0 + - - -
272A TYR* 3.6 10.9 - - - -
273A CSO 3.4 25.9 + - - -
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Residues in contact with TYR 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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16A LEU* 2.8 37.3 + - + +
19A VAL* 3.9 15.5 - - + -
28A VAL* 4.7 0.9 - - + -
67A GLY 3.1 4.4 + - - -
68A GLN* 1.3 74.3 - - - +
70A TYR* 1.3 75.4 + + - +
72A LEU* 3.1 11.1 + - + +
73A LEU* 3.0 50.8 + - + +
99A GLN* 3.8 24.1 + - + +
102A GLU* 3.3 52.9 - - + -
103A THR* 3.4 17.3 - - - +
106A LEU* 3.8 19.9 - - + +
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.4 37.4 + - + +
21A GLY 5.5 2.5 - - - -
22A SER* 3.8 23.9 - - - -
23A LYS 4.2 2.0 - - - -
24A PRO* 3.6 35.4 - - + -
25A GLY 3.6 7.4 - - - -
26A LYS* 2.7 35.6 + - - +
68A GLN 3.3 1.0 - - - -
69A TYR* 1.3 82.9 - + - +
71A ASP* 1.3 60.8 + - - +
73A LEU* 3.7 19.0 + - + +
74A ARG* 3.1 27.7 + - - +
99A GLN* 3.1 29.8 - - - -
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Residues in contact with ASP 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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65A ILE* 5.6 1.6 - - + -
68A GLN* 2.8 40.7 + - + +
70A TYR* 1.3 79.3 - - - +
72A LEU* 1.3 60.1 + - - +
73A LEU 3.4 0.2 - - - -
74A ARG* 3.3 28.9 + - + +
75A LEU* 2.9 34.1 + - - +
268A SER 4.7 3.4 - - - +
269A ALA* 5.1 0.4 - - - -
270A PRO* 3.7 27.9 - - + +
296A LEU* 5.1 0.5 - - - +
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Residues in contact with LEU 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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65A ILE* 4.2 15.1 - - + +
68A GLN 3.1 8.2 + - - +
69A TYR* 3.1 15.6 + - + +
71A ASP* 1.3 73.3 - - - +
73A LEU* 1.3 66.1 + - - +
75A LEU* 3.2 15.3 + - + +
76A PHE* 3.2 49.3 + - + -
89A PHE* 3.8 29.8 - - + -
103A THR* 3.8 34.8 - - + +
106A LEU* 4.2 14.8 - - + -
107A LEU* 4.0 15.0 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU 4.7 1.3 - - - +
17A LEU* 3.8 25.1 - - + -
19A VAL* 4.4 3.8 - - + -
20A ARG* 4.3 31.2 - - + +
21A GLY 5.5 0.2 - - - +
69A TYR* 3.0 53.7 + - + +
70A TYR* 3.8 32.8 - - + +
72A LEU* 1.3 75.1 - - - +
74A ARG* 1.3 62.4 + - - +
76A PHE* 3.3 7.9 + - + +
77A GLU* 3.1 27.1 + - - +
81A PHE* 3.9 5.9 - - + -
106A LEU* 3.9 8.7 - - + -
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Residues in contact with ARG 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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70A TYR 3.1 18.8 + - - +
71A ASP* 3.4 22.9 + - - +
72A LEU 3.2 0.2 - - - -
73A LEU* 1.3 73.6 - - - +
75A LEU* 1.3 66.7 + - - +
77A GLU* 3.0 23.3 + - - +
78A TYR* 3.0 64.0 + - - -
270A PRO* 3.6 24.9 - - - +
296A LEU* 3.9 16.8 - - + +
297A LYS 2.7 30.9 + - - +
298A PRO* 4.2 3.0 - - - +
299A ALA* 4.4 13.0 - - - +
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Residues in contact with LEU 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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62A CYS* 4.3 12.3 - - - -
65A ILE* 3.4 32.8 - - + -
71A ASP 2.9 20.0 + - - +
72A LEU* 3.2 17.2 + - + +
74A ARG* 1.3 75.2 - - - +
76A PHE* 1.3 55.2 + - + +
78A TYR* 3.3 0.4 + - - -
79A GLY* 2.7 34.3 + - - -
87A TYR* 4.0 1.9 + - + -
89A PHE* 4.6 1.3 - - + -
268A SER* 3.8 28.5 - - - +
281A ALA 4.6 2.5 - - - +
282A MET* 3.5 33.7 - - + +
296A LEU* 4.1 24.9 - - + +
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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 LEU* 3.2 39.7 + - + -
73A LEU* 3.7 2.7 - - - +
74A ARG 3.1 1.2 - - - -
75A LEU* 1.3 80.5 - - + +
77A GLU* 1.3 54.7 + - - +
80A GLY* 2.6 36.0 + - - -
81A PHE* 3.4 36.1 + + + -
82A PRO* 3.8 14.6 - - + -
87A TYR* 3.6 45.1 - + - -
89A PHE* 3.9 18.8 - + - -
106A LEU* 4.1 11.2 - - + -
107A LEU* 4.5 1.3 - - + -
110A TYR* 3.9 18.4 - + - -
118A PHE* 3.9 18.8 - + - -
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Residues in contact with GLU 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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20A ARG* 3.3 37.3 + - - +
21A GLY* 5.4 2.1 + - - -
73A LEU* 3.1 17.1 + - - +
74A ARG* 3.0 35.2 + - - +
76A PHE* 1.3 77.6 - - - +
78A TYR* 1.3 67.8 + - + +
80A GLY* 4.4 2.2 + - - -
81A PHE* 3.6 14.5 - - + -
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Residues in contact with TYR 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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74A ARG* 3.0 52.1 + - - +
75A LEU 3.7 6.3 - - - +
77A GLU* 1.3 85.9 - - + +
79A GLY* 1.3 60.9 + - - +
80A GLY 3.4 0.6 + - - -
282A MET* 4.0 10.8 - - + -
294A GLN* 3.2 27.7 + - + +
295A ILE 3.6 21.1 + - - -
296A LEU* 3.5 31.6 - - + -
297A LYS 5.2 0.5 + - - -
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Residues in contact with GLY 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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60A LYS* 3.6 11.2 + - - -
75A LEU 2.7 16.7 + - - -
78A TYR* 1.3 74.0 - - - +
80A GLY* 1.3 51.0 + - - +
84A GLU* 4.7 1.4 - - - +
85A SER* 2.7 27.4 + - - -
87A TYR* 3.1 16.9 + - - -
282A MET* 3.6 16.1 - - - +
294A GLN* 4.3 6.7 - - - -
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Residues in contact with GLY 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* 2.6 18.4 + - - +
77A GLU 4.4 2.1 + - - -
78A TYR 3.4 2.4 - - - -
79A GLY* 1.3 74.9 - - - +
81A PHE* 1.3 65.5 + - - -
82A PRO* 4.0 0.3 - - - +
84A GLU* 3.9 23.1 - - - -
85A SER* 4.2 2.5 - - - -
87A TYR* 2.4 31.0 + - - -
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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