Contacts of the helix formed by residues 89 - 109 (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 ASP 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ASN 4.2 1.2 + - - -
88A THR* 1.3 75.1 - - - +
90A VAL* 1.3 68.1 + - - +
91A GLN* 3.5 10.8 + - - +
92A THR* 2.9 41.7 + - - +
93A TYR* 3.0 20.4 + - - +
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Residues in contact with VAL 90 (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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84A VAL* 3.7 31.4 - - + -
88A THR 3.4 3.3 + - - +
89A ASP* 1.3 75.8 + - - +
91A GLN* 1.3 66.8 + - + +
93A TYR* 3.1 8.8 + - + +
94A ARG* 2.9 59.8 + - + +
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Residues in contact with GLN 91 (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 TYR* 4.7 3.8 - - - +
77A ARG* 2.6 40.0 + - - +
89A ASP* 3.4 10.8 + - - +
90A VAL* 1.3 78.9 - - + +
92A THR* 1.3 66.6 + - - +
94A ARG* 3.3 10.2 + - - +
95A HIS* 3.0 43.2 + - + -
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Residues in contact with THR 92 (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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49A ALA* 3.6 31.0 - - + +
50A LYS* 3.8 20.0 - - + +
53A ALA* 3.8 15.3 - - + +
57A TYR* 4.5 7.8 + - - -
88A THR* 5.4 2.0 - - + -
89A ASP* 2.9 32.7 + - + +
91A GLN* 1.3 76.9 - - - +
93A TYR* 1.3 56.9 + - - +
95A HIS 3.4 0.2 + - - -
96A SER* 3.0 27.6 + - - -
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Residues in contact with TYR 93 (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 LEU* 6.1 0.5 - - - +
49A ALA* 4.6 9.4 - - + -
80A ASN* 3.5 43.3 + - + -
83A THR 4.1 8.2 + - - -
84A VAL* 4.3 13.5 - - + -
85A PRO* 3.5 41.4 - - + +
88A THR* 4.0 13.0 - - + +
89A ASP 3.0 13.0 + - - +
90A VAL* 3.3 11.7 - - - +
92A THR* 1.3 77.7 - - - +
94A ARG* 1.3 56.4 + - + +
96A SER* 3.3 8.9 + - - -
97A THR* 2.9 47.1 + - - -
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Residues in contact with ARG 94 (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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77A ARG* 3.4 69.6 - - + +
78A ASN* 3.9 13.7 + - - -
79A ALA* 4.7 6.2 - - - +
80A ASN* 2.9 31.7 - - - +
82A GLY* 6.1 2.0 - - - -
84A VAL* 5.8 2.6 - - - +
90A VAL* 2.9 38.7 + - + +
91A GLN* 3.3 10.7 + - - +
93A TYR* 1.3 77.3 - - + +
95A HIS* 1.3 57.8 + - - +
97A THR* 3.7 1.5 - - - -
98A ALA* 2.9 28.1 + - - +
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Residues in contact with HIS 95 (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 ALA* 4.0 18.2 - - + -
56A VAL* 3.4 32.4 - - + +
57A TYR* 3.6 32.7 - + + -
60A LEU* 4.8 11.7 - - + -
77A ARG* 4.1 20.5 + - - +
91A GLN* 3.0 45.3 + - + +
92A THR 3.9 2.9 - - - +
94A ARG* 1.3 72.8 - - - +
96A SER* 1.3 65.0 + - - +
98A ALA* 3.3 6.4 + - - +
99A PHE 3.0 18.2 + - - -
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Residues in contact with SER 96 (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 VAL 5.2 0.2 + - - -
48A SER 4.5 0.2 - - - -
49A ALA* 3.4 33.5 - - - +
52A GLN* 2.9 34.5 + - - +
53A ALA* 4.3 2.5 - - - +
92A THR 3.0 14.7 + - - -
93A TYR* 3.4 11.7 - - - -
95A HIS* 1.3 77.0 - - - +
97A THR* 1.3 63.0 + - - +
99A PHE* 3.1 14.6 + - - +
100A GLU* 3.2 13.3 + - - +
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Residues in contact with THR 97 (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 5.4 2.0 - - - +
10A LEU* 5.9 6.5 - - + -
13A ALA* 3.7 17.1 - - + +
76A GLY 3.0 18.2 - - - +
77A ARG 4.5 0.4 - - - -
80A ASN* 3.7 21.8 + - + +
93A TYR* 2.9 38.3 + - - -
94A ARG 3.7 4.3 - - - -
96A SER* 1.3 72.8 + - - +
98A ALA* 1.3 62.9 + - - +
100A GLU* 3.2 16.0 + - - +
101A ALA* 3.0 19.6 + - - +
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Residues in contact with ALA 98 (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* 5.2 0.9 - - + -
73A LEU* 3.2 47.7 - - + +
76A GLY* 3.6 10.7 + - - -
77A ARG* 3.7 7.0 - - + +
94A ARG 2.9 17.9 + - - +
95A HIS* 3.4 11.2 - - - +
96A SER 3.2 0.2 - - - -
97A THR* 1.3 78.0 - - - +
99A PHE* 1.3 62.5 + - - +
101A ALA* 3.1 4.0 + - - +
102A LEU* 3.1 18.0 + - - +
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Residues in contact with PHE 99 (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 TYR* 3.7 46.2 - + - -
52A GLN* 3.8 30.3 - - + -
55A VAL* 3.7 26.2 - - + -
56A VAL* 3.6 19.3 - - + -
59A LEU* 4.7 5.2 - - + -
73A LEU* 3.8 9.3 - - + +
95A HIS 3.0 7.2 + - - +
96A SER 3.1 9.4 + - - +
98A ALA* 1.3 73.6 - - - +
100A GLU* 1.3 66.5 + - + +
102A LEU* 3.2 9.3 + - + +
103A ILE* 3.1 51.4 + - + +
118A ILE* 4.3 13.0 - - + -
119A VAL* 5.4 0.7 - - + -
122A ALA* 4.0 12.8 - - + -
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Residues in contact with GLU 100 (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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12A LEU 3.5 1.2 - - - +
13A ALA* 3.6 25.6 - - - +
16A GLY* 3.2 12.4 - - - +
17A ASP* 3.8 39.0 - - - +
20A TYR* 5.9 1.1 - - + -
47A VAL 5.2 1.2 - - - +
52A GLN* 3.0 32.4 + - - +
96A SER* 3.2 8.5 + - - +
97A THR* 3.5 19.7 + - - +
98A ALA 3.2 0.4 - - - -
99A PHE* 1.3 78.9 - - + +
101A ALA* 1.3 55.9 + - - +
103A ILE* 3.3 4.5 + - - -
104A GLY 2.9 24.4 + - - -
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Residues in contact with ALA 101 (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* 4.0 18.2 - - - +
12A LEU* 3.8 10.8 - - + +
13A ALA* 3.7 11.3 - - - +
72A VAL* 3.9 11.1 - - + +
76A GLY* 3.9 21.3 - - - -
97A THR 3.0 12.7 + - - +
98A ALA 3.1 7.8 + - - +
100A GLU* 1.3 76.2 - - - +
102A LEU* 1.3 57.1 + - - +
104A GLY* 3.8 0.5 - - - -
105A TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 102 (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 5.2 - - + -
65A LEU* 4.0 33.2 - - + -
69A GLU* 3.9 37.7 - - + +
72A VAL* 3.7 15.4 - - + +
73A LEU* 4.2 15.0 - - + -
98A ALA 3.1 11.0 + - - +
99A PHE* 3.5 11.4 - - + +
101A ALA* 1.3 75.0 - - - +
103A ILE* 1.3 66.4 + - + +
105A TYR* 3.3 5.6 + - + +
106A HIS* 3.2 31.2 + - + +
118A ILE* 4.1 22.0 - - + -
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Residues in contact with ILE 103 (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 GLY* 3.6 15.3 - - - +
19A VAL* 3.6 28.5 - - + -
20A TYR* 4.0 9.6 - - + +
99A PHE* 3.1 47.3 + - + +
100A GLU* 3.7 6.7 - - - +
102A LEU* 1.3 79.9 - - + +
104A GLY* 1.3 62.0 + - - +
105A TYR 3.3 0.2 + - - -
106A HIS 3.4 0.3 + - - -
107A HIS* 3.1 20.8 + - - +
115A LEU* 3.8 25.2 - - + +
118A ILE* 3.9 19.3 - - + -
119A VAL* 4.0 10.1 - - + -
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Residues in contact with GLY 104 (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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12A LEU* 3.4 26.9 - - - -
15A MSE 4.2 7.4 - - - -
16A GLY* 3.4 11.8 - - - -
100A GLU 2.9 10.9 + - - -
103A ILE* 1.3 77.1 - - - +
105A TYR* 1.3 57.0 + - - +
107A HIS* 3.3 3.7 + - - +
108A LEU* 2.9 36.6 + - - +
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Residues in contact with TYR 105 (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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4A ALA* 3.9 26.4 - - + +
5A LYS* 3.7 26.8 - - - +
12A LEU* 3.8 18.1 - - + +
68A GLU* 2.8 36.0 + - + +
69A GLU* 5.7 1.8 - - + -
72A VAL* 3.9 35.0 - - + -
101A ALA 2.9 17.5 + - - +
102A LEU* 3.4 7.4 - - + +
104A GLY* 1.3 76.7 - - - +
106A HIS* 1.3 83.5 + + - +
108A LEU* 3.4 2.1 + - - +
109A LEU* 3.1 49.2 + - + +
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Residues in contact with HIS 106 (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 GLU* 5.6 2.5 - - - -
69A GLU* 2.7 35.4 + - + +
102A LEU* 3.2 24.5 + - + +
105A TYR* 1.3 91.0 - + - +
107A HIS* 1.3 63.8 + - - +
109A LEU 3.4 0.9 + - - -
110A ASN 3.1 2.8 + - - -
111A ASN* 2.9 65.5 + - + +
114A ARG* 3.8 14.9 - - + +
115A LEU* 4.1 24.9 - - + -
118A ILE* 3.7 24.0 - - + -
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Residues in contact with HIS 107 (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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15A MSE 4.1 24.1 - - + +
19A VAL* 3.5 37.9 - - + +
103A ILE 3.1 14.9 + - - +
104A GLY* 3.5 7.9 - - - +
106A HIS* 1.3 77.9 - - - +
108A LEU* 1.3 65.3 + - + +
110A ASN* 3.0 26.0 + - - +
115A LEU* 3.8 13.8 - - + +
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Residues in contact with LEU 108 (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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2A ILE* 3.8 44.2 - - + +
4A ALA* 4.0 14.1 - - + -
7A LEU* 3.7 29.6 - - + -
12A LEU* 4.1 9.9 - - + -
15A MSE 4.1 33.9 - - + -
104A GLY 2.9 19.3 + - - +
107A HIS* 1.3 83.2 - - + +
109A LEU* 1.3 62.0 + - - +
110A ASN* 3.3 9.0 + - - +
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Residues in contact with LEU 109 (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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2A ILE 5.9 1.3 - - - +
4A ALA* 3.7 19.3 - - + +
5A LYS* 4.5 20.6 - - + -
68A GLU* 5.1 1.3 - - - +
105A TYR* 3.1 58.8 + - + +
106A HIS 4.1 0.2 - - - +
107A HIS 3.2 0.4 - - - -
108A LEU* 1.3 77.8 - - - +
110A ASN* 1.3 71.2 + - - +
111A ASN* 3.2 29.3 + - - +
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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