Contacts of the helix formed by residues 66 - 75 (chain A) in PDB entry 1U1H
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 ASP 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.9 2.2 - - - +
63A ALA* 4.0 5.1 - - - +
65A TYR* 1.3 84.6 - - + +
67A GLN* 1.3 64.3 + - - +
68A VAL* 2.9 14.7 + - - +
69A LEU* 2.8 25.7 + - + +
70A ASP* 2.9 29.8 + - - -
94A TYR* 3.2 5.2 + - - -
117A TYR* 2.7 25.6 + - - +
118A HIS 4.9 1.1 - - - +
119A TYR* 3.2 27.1 - - - +
120A ILE* 3.2 26.6 + - + -
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Residues in contact with GLN 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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10A ARG* 3.0 33.3 + - - +
60A ASN 5.9 2.7 - - - +
61A THR 5.6 2.0 - - - +
63A ALA* 4.2 1.9 - - + +
66A ASP* 1.3 74.8 - - - +
68A VAL* 1.3 72.8 + - + +
70A ASP* 3.0 32.2 - - - +
71A THR* 3.0 12.7 - - - +
112A TRP* 4.0 29.2 - - + +
117A TYR* 3.3 20.1 + - - -
156A VAL* 4.5 12.8 - - + +
331A LEU* 5.1 7.9 - - - +
332A HIS* 5.4 1.2 + - - -
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Residues in contact with VAL 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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66A ASP* 2.9 11.2 + - - +
67A GLN* 1.3 76.7 - - + +
69A LEU* 1.3 64.7 + - - +
71A THR* 3.0 12.6 + - - +
72A THR* 2.9 20.1 + - - -
112A TRP* 3.6 27.1 - - + -
119A TYR* 3.6 29.2 - - + -
120A ILE 3.5 16.2 - - - +
122A PRO* 3.8 22.4 - - + -
156A VAL* 4.8 5.4 - - + -
161A TYR* 4.1 10.9 - - + -
164A LEU* 4.8 8.3 - - + -
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Residues in contact with LEU 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 TYR* 4.5 2.5 - - + -
66A ASP* 2.8 25.5 + - + +
67A GLN 3.3 0.2 - - - -
68A VAL* 1.3 76.7 - - - +
70A ASP* 1.3 62.1 + - - +
72A THR* 3.1 10.8 + - + -
73A ALA* 3.0 17.7 + - - +
94A TYR* 3.4 34.5 - - + +
97A MSE 3.5 36.8 - - + -
98A ALA* 3.6 31.2 - - + +
107A MSE 4.8 3.4 - - - -
120A ILE* 4.0 24.2 + - + -
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Residues in contact with ASP 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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60A ASN* 4.9 9.1 + - - +
62A PHE 3.6 2.4 - - - +
63A ALA* 3.3 23.6 - - - +
64A HIS 4.8 0.5 + - - -
66A ASP 2.9 15.7 + - - +
67A GLN* 3.0 16.5 + - - +
69A LEU* 1.3 76.1 - - - +
71A THR* 1.3 56.1 + - - +
73A ALA* 3.1 6.2 + - - +
74A MSE 3.0 25.7 + - - +
94A TYR* 2.7 33.8 + - - -
134A SER* 4.8 2.4 + - - -
136A LYS* 3.5 33.9 + - + +
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Residues in contact with THR 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 GLN 3.0 18.3 + - - +
68A VAL* 3.1 18.4 - - - +
70A ASP* 1.3 75.6 - - - +
72A THR* 1.3 55.4 + - - +
74A MSE 3.4 15.6 - - - +
75A LEU* 3.0 37.2 + - - +
156A VAL* 3.7 30.3 - - + -
161A TYR* 3.1 26.4 - - + -
188A TYR* 4.1 7.3 + - - -
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Residues in contact with THR 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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68A VAL 2.9 14.4 + - - -
69A LEU* 3.3 17.0 - - + +
70A ASP 3.1 0.2 - - - -
71A THR* 1.3 79.7 + - - +
73A ALA* 1.3 60.3 + - - +
75A LEU* 3.4 1.8 + - - -
76A GLY* 3.1 2.8 + - - -
77A ALA 3.1 52.5 + - - +
78A VAL* 6.0 0.2 - - - +
97A MSE 4.1 20.0 - - - -
107A MSE 4.8 9.4 - - + -
120A ILE 5.3 0.5 + - - -
122A PRO* 3.5 16.5 - - + +
161A TYR* 3.0 24.2 + - - +
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Residues in contact with ALA 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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69A LEU 3.0 11.8 + - - +
70A ASP* 3.5 9.6 - - - +
72A THR* 1.3 75.1 - - - +
74A MSE 1.3 66.1 + - - +
76A GLY 3.0 9.5 + - - -
89A ILE* 3.6 28.0 - - + +
94A TYR* 4.4 14.8 - - + -
97A MSE 4.6 5.4 - - + -
133A ALA* 3.4 13.5 - - - +
134A SER* 3.4 23.5 - - - +
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Residues in contact with MSE 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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60A ASN* 5.1 2.5 - - - +
70A ASP 3.0 13.2 + - - +
71A THR* 3.4 19.3 - - - +
73A ALA* 1.3 78.3 - - - +
75A LEU* 1.3 62.8 + - + +
76A GLY 3.3 0.4 - - - -
131A SER 3.3 9.5 - - - +
132A TYR* 3.5 8.6 - - + +
133A ALA 3.4 7.1 + - - -
134A SER* 3.6 27.1 - - - +
136A LYS* 6.4 0.2 - - + -
137A ALA* 3.8 14.6 - - + +
155A LEU* 3.2 39.0 - - + -
187A ILE* 3.6 5.7 - - + +
188A TYR* 5.2 12.1 - - - -
191A VAL* 3.4 39.3 - - + -
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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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71A THR* 3.0 24.3 + - - +
72A THR 3.4 3.1 + - - +
73A ALA 3.1 0.2 - - - -
74A MSE 1.3 81.5 - - + +
76A GLY* 1.3 62.0 + - - +
77A ALA* 2.9 7.3 + - + +
130A PHE* 3.3 18.7 - - + +
131A SER 2.9 24.3 + - - -
161A TYR* 3.5 37.0 - - + -
184A ILE* 4.0 25.4 - - + +
187A ILE* 3.7 34.8 - - + -
188A TYR* 4.0 19.5 - - + -
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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