Contacts of the helix formed by residues 84 - 97 (chain A) in PDB entry 1UOU
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 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 5.9 4.0 - - - +
83A MET* 1.3 74.2 - - - +
85A LEU* 1.3 81.4 + - - +
86A GLU* 3.3 3.8 - - + +
87A GLU* 2.9 32.1 + - + +
88A THR* 3.1 11.5 + - - -
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Residues in contact with LEU 85 (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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83A MET 6.0 0.2 - - - +
84A ASP* 1.3 87.6 + - - +
86A GLU* 1.3 62.8 + - - +
88A THR* 3.8 8.2 - - - +
89A SER* 3.0 26.3 + - - -
254A THR* 4.3 18.8 - - + +
258A VAL* 4.1 25.4 - - + +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.2 22.7 + - - +
84A ASP* 3.3 2.3 - - + +
85A LEU* 1.3 79.1 - - - +
87A GLU* 1.3 58.4 + - - +
89A SER* 3.5 5.7 - - - -
90A VAL* 3.1 38.9 + - - +
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Residues in contact with GLU 87 (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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43A LYS* 2.7 33.5 + - - -
48A ARG* 3.4 29.4 + - - +
49A LEU* 2.8 40.3 + - - +
54A ILE* 4.4 3.4 - - + +
83A MET* 3.5 23.7 - - + +
84A ASP* 2.9 26.5 + - - +
86A GLU* 1.3 79.2 - - - +
88A THR* 1.3 58.7 + - - +
90A VAL* 3.3 7.0 + - - +
91A LEU* 2.9 28.2 + - - +
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Residues in contact with THR 88 (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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83A MET* 4.0 8.8 + - - +
84A ASP 3.1 15.2 + - - -
85A LEU* 3.8 12.2 - - - +
87A GLU* 1.3 72.2 - - - +
89A SER* 1.3 60.7 + - - +
91A LEU* 3.1 8.8 + - - +
92A THR* 2.8 34.9 + - - +
212A PRO* 3.5 39.9 - - + +
215A THR* 3.7 30.5 - - + -
254A THR* 5.2 3.0 - - + +
258A VAL* 4.5 7.4 - - + -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 3.0 18.3 + - - -
86A GLU* 3.5 10.0 + - - -
88A THR* 1.3 76.7 - - - +
90A VAL* 1.3 62.3 + - - -
92A THR* 3.2 5.6 + - - -
93A GLN* 3.0 35.2 + - - +
258A VAL* 4.1 19.2 - - - +
261A SER* 4.6 7.3 + - - -
262A LEU* 4.0 16.0 - - - +
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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
----------------------------------------------------------
48A ARG* 6.1 0.4 - - - +
50A SER 5.6 0.9 - - - +
51A GLU* 3.7 49.1 - - + +
54A ILE* 4.0 17.9 - - + -
55A ARG* 5.1 6.7 - - + +
86A GLU* 3.1 32.4 + - - +
87A GLU* 3.8 5.6 - - - +
88A THR 3.3 0.2 - - - -
89A SER* 1.3 72.4 - - - +
91A LEU* 1.3 66.1 + - - +
93A GLN* 3.3 18.4 + - + +
94A ALA* 2.9 21.9 + - + +
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Residues in contact with LEU 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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54A ILE* 3.8 15.2 - - + +
57A PHE* 6.0 2.5 - - + -
58A VAL* 4.3 14.4 - - + -
78A ILE* 5.2 3.6 - - + -
83A MET* 3.9 23.1 - - + -
87A GLU 2.9 14.6 + - - +
88A THR* 3.1 10.3 + - - +
90A VAL* 1.3 74.5 - - - +
92A THR* 1.3 58.2 + - - +
94A ALA* 3.2 2.3 + - - +
95A LEU* 3.0 58.9 + - + +
198A LEU* 4.7 7.4 - - + -
212A PRO* 4.2 5.4 - - + +
213A LEU* 3.9 26.9 - - + -
216A ALA* 3.9 17.0 - - + -
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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
----------------------------------------------------------
88A THR* 2.8 20.3 + - - +
89A SER* 3.3 9.7 - - - -
91A LEU* 1.3 73.9 - - - +
93A GLN* 1.3 64.9 - - - +
96A ALA* 3.0 25.3 + - - +
215A THR 4.2 1.9 + - - -
216A ALA* 3.2 25.4 + - - +
219A LEU* 3.5 17.1 - - + +
220A SER* 3.5 29.7 - - - +
223A LEU* 4.1 12.1 - - + -
258A VAL* 4.5 3.5 - - + +
262A LEU* 4.1 9.6 - - + -
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Residues in contact with GLN 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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51A GLU* 5.3 4.8 + - - -
55A ARG* 4.4 8.3 + - - +
89A SER* 3.0 28.7 + - - +
90A VAL* 3.6 24.8 - - + +
92A THR* 1.3 75.9 - - - +
94A ALA* 1.3 56.0 + - - +
96A ALA* 3.5 5.5 - - - +
97A GLN* 3.0 54.7 + - - +
223A LEU* 6.6 0.2 - - - -
262A LEU* 3.5 29.5 - - + +
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Residues in contact with ALA 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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54A ILE* 4.4 9.0 - - + -
55A ARG* 4.2 28.6 + - + +
58A VAL* 3.7 30.2 - - + +
90A VAL 2.9 17.3 + - - +
91A LEU 3.5 5.2 - - - +
92A THR 3.2 0.2 - - - -
93A GLN* 1.3 75.8 - - - +
95A LEU* 1.3 59.1 + - - +
97A GLN* 3.5 1.6 + - - +
98A SER* 3.1 26.2 + - - -
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Residues in contact with LEU 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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58A VAL* 4.1 9.9 - - + -
91A LEU* 3.0 35.3 + - + +
94A ALA* 1.3 72.4 - - - +
96A ALA* 1.3 65.0 + - - +
98A SER* 2.9 24.1 + - - -
192A VAL* 3.5 18.9 - - + +
194A ALA* 3.7 26.9 - - + -
195A ASP* 4.5 9.9 - - + +
198A LEU* 4.0 26.0 - - + -
213A LEU 5.8 0.2 - - - +
216A ALA* 3.8 27.1 - - + +
217A SER* 4.4 2.5 - - - +
220A SER* 3.7 14.4 - - - +
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Residues in contact with ALA 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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92A THR 3.0 18.7 + - - +
93A GLN* 3.5 8.5 - - - +
95A LEU* 1.3 78.9 - - - +
97A GLN* 1.3 61.2 + - + +
98A SER 3.7 0.2 + - - -
99A GLY* 3.6 14.0 + - - +
100A GLN 4.2 1.6 - - - +
101A GLN* 5.5 3.0 - - - +
192A VAL* 4.6 2.7 + - - +
220A SER* 3.8 14.6 - - - +
223A LEU* 4.5 9.9 - - + -
224A VAL* 3.4 35.8 - - + +
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Residues in contact with GLN 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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55A ARG* 3.0 36.6 + - - +
93A GLN* 3.0 39.2 + - - +
94A ALA 3.5 4.5 + - - +
95A LEU 3.2 0.2 - - - -
96A ALA* 1.3 76.2 - - + +
98A SER* 1.3 58.8 + - - +
99A GLY 3.0 15.3 + - - +
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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