Contacts of the helix formed by residues 66 - 77 (chain A) in PDB entry 1U61
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE 5.7 0.2 - - - +
65A LEU* 1.3 75.2 - - - +
67A GLU* 1.3 61.0 + - - +
68A GLU* 3.6 9.1 + - - +
69A GLU* 3.0 36.2 + - - +
70A GLU* 2.9 26.8 + - - +
114A ARG* 4.7 7.2 - - - +
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Residues in contact with GLU 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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66A THR* 1.3 72.6 - - - +
68A GLU* 1.3 68.6 + - + +
70A GLU* 3.2 9.9 + - - +
71A ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 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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5A LYS* 4.4 15.4 + - - -
66A THR* 3.3 8.4 + - - +
67A GLU* 1.3 81.8 - - + +
69A GLU* 1.3 63.7 + - + +
71A ALA* 3.1 9.2 + - - +
72A VAL* 3.1 21.8 + - + +
105A TYR* 2.8 37.5 + - + +
106A HIS* 5.6 2.3 - - - -
109A LEU* 5.1 1.4 - - - +
111A ASN* 5.9 0.7 + - - -
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Residues in contact with GLU 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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65A LEU* 3.3 18.9 - - + +
66A THR* 3.0 32.4 + - - +
68A GLU* 1.3 79.4 - - + +
70A GLU* 1.3 62.4 + - - +
72A VAL* 3.3 8.0 + - - +
73A LEU* 3.2 23.6 + - - +
102A LEU* 3.9 17.8 - - + +
105A TYR* 5.7 1.8 - - + -
106A HIS* 2.7 36.2 + - + +
114A ARG* 2.8 44.3 + - - +
118A ILE* 3.8 2.8 - - - +
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Residues in contact with GLU 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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59A LEU 4.9 0.2 - - - +
60A LEU* 3.9 37.6 - - + +
63A ALA* 4.7 9.2 - - - +
65A LEU* 3.9 23.9 - - + +
66A THR 2.9 20.4 + - - +
67A GLU* 3.2 8.5 + - - +
69A GLU* 1.3 75.7 - - - +
71A ALA* 1.3 57.6 + - - +
73A LEU* 3.4 9.1 + - - +
74A ARG* 2.9 28.1 + - - +
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Residues in contact with ALA 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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67A GLU 3.0 12.4 + - - +
68A GLU* 3.1 11.4 + - - +
70A GLU* 1.3 74.6 - - - +
72A VAL* 1.3 64.8 + - - +
74A ARG* 3.3 29.1 + - - +
75A ARG* 2.9 32.0 + - + +
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Residues in contact with VAL 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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9A SER* 4.7 0.7 + - - +
12A LEU* 4.8 6.3 - - + -
68A GLU* 3.1 15.2 + - + +
69A GLU* 3.5 10.3 - - - +
71A ALA* 1.3 76.1 - - - +
73A LEU* 1.3 51.8 + - - +
75A ARG* 3.4 8.1 + - - +
76A GLY* 2.8 31.4 + - - -
101A ALA* 3.9 10.7 - - + +
102A LEU* 3.7 34.1 - - + +
105A TYR* 3.9 45.8 - - + +
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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
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56A VAL* 4.0 25.8 - - + +
59A LEU* 5.4 1.3 - - + -
60A LEU* 3.8 24.2 - - + -
65A LEU* 3.5 28.9 - - + -
69A GLU 3.2 12.9 + - - +
70A GLU* 3.5 9.0 - - - +
72A VAL* 1.3 73.4 - - - +
74A ARG* 1.3 69.3 + - - +
76A GLY 3.0 8.8 + - - -
77A ARG* 3.3 4.6 + - - +
98A ALA* 3.2 52.7 - - + +
99A PHE* 3.8 10.1 - - + +
102A LEU* 4.2 13.9 - - + -
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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 GLU 2.9 17.7 + - - +
71A ALA* 3.6 29.2 - - - +
73A LEU* 1.3 76.6 - - - +
75A ARG* 1.3 87.3 + - - +
76A GLY 3.3 0.2 + - - -
77A ARG* 3.5 11.5 + - - +
78A ASN* 2.9 25.2 + - - +
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Residues in contact with ARG 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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9A SER* 3.1 22.7 + - - +
71A ALA* 2.9 22.2 + - + +
72A VAL* 3.6 6.5 - - - +
74A ARG* 1.3 99.9 - - - +
76A GLY* 1.3 62.2 + - - +
78A ASN* 3.1 22.9 + - - +
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Residues in contact with GLY 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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9A SER* 3.5 15.4 - - - -
72A VAL 2.8 17.3 + - - -
73A LEU 3.0 4.9 + - - -
75A ARG* 1.3 72.7 - - - +
77A ARG* 1.3 62.9 + - - +
78A ASN 2.8 7.6 + - - -
97A THR* 3.0 24.4 - - - +
98A ALA* 3.7 8.3 - - - -
101A ALA* 3.9 14.4 - - - -
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Residues in contact with ARG 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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73A LEU 3.3 9.7 + - - +
74A ARG* 3.5 15.0 + - - +
75A ARG 3.2 0.4 - - - -
76A GLY* 1.3 76.8 - - - +
78A ASN* 1.3 74.7 + - - +
80A ASN* 2.9 30.9 + - - +
91A GLN* 2.6 38.8 + - - +
94A ARG* 3.4 63.6 - - + +
95A HIS* 4.1 21.7 + - - +
98A ALA* 3.7 3.3 - - + +
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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
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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