Contacts of the helix formed by residues 90 - 97 (chain B) in PDB entry 1UMD
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 GLY 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASP* 5.8 0.2 - - - -
60B GLU* 3.7 11.0 - - - +
61B ALA* 3.6 25.6 - - - -
64B VAL* 4.3 6.0 - - - +
87B ILE* 2.9 12.4 + - - -
89B PRO* 1.3 77.9 - - - +
91B PHE* 1.3 63.2 + - - +
92B ASP 3.4 2.7 - - - -
93B GLN* 3.3 6.9 + - - +
94B LEU* 3.1 21.4 + - - +
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.1 12.8 + - + -
88B PHE* 2.9 38.5 + + - +
89B PRO 3.4 0.6 - - - -
90B GLY* 1.3 75.1 - - - +
92B ASP* 1.3 66.2 + - - +
94B LEU* 3.2 5.5 + - + +
95B VAL* 2.9 46.1 + - + +
136B HIS* 3.9 22.4 - - + -
137B PHE* 4.4 11.2 - + - -
88D PHE* 3.5 41.1 - + - +
91D PHE* 3.7 31.6 - + + -
136D HIS* 3.8 25.1 - + - -
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO* 3.6 11.9 - - - +
146A ILE 5.6 0.5 - - - +
148A SER* 3.6 27.2 - - - -
182A ASP* 4.5 11.0 - - - +
89B PRO 5.3 0.4 + - - -
90B GLY 3.4 0.8 - - - -
91B PHE* 1.3 78.7 - - - +
93B GLN* 1.3 57.5 + - - +
95B VAL* 4.1 1.1 - - - -
96B SER* 2.6 60.0 + - - -
97B GLN* 3.5 0.3 + - - +
85D ASP 4.8 1.2 - - - +
88D PHE* 3.4 28.2 + - + +
89D PRO* 3.9 30.3 - - + +
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 2.9 41.1 + - - +
151A PRO* 3.6 11.9 - - + +
152A PRO* 3.5 8.7 - - - +
182A ASP* 3.1 25.4 + - - +
61B ALA* 3.4 25.4 - - + +
64B VAL* 3.8 17.3 - - + -
65B GLY* 3.1 21.4 - - - +
90B GLY 3.3 10.4 + - - +
91B PHE 3.2 0.4 - - - -
92B ASP* 1.3 77.6 + - - +
94B LEU* 1.3 59.1 + - - +
97B GLN* 3.2 14.0 + - - +
98B VAL* 2.9 28.6 + - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 3.7 15.9 - - + +
87B ILE* 4.0 19.3 - - + -
90B GLY 3.1 10.2 + - - +
91B PHE* 3.2 10.5 + - + +
93B GLN* 1.3 81.2 - - - +
95B VAL* 1.3 64.6 + - + +
98B VAL* 3.3 13.3 - - + +
99B ALA* 3.0 28.8 + - - +
115B VAL* 4.6 11.7 - - + -
117B MET* 5.7 0.4 - - + -
137B PHE* 3.6 37.5 - - + -
143B LEU* 4.0 27.1 - - + -
169B VAL* 4.3 12.8 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 2.9 46.8 + - + +
92B ASP* 4.0 1.1 - - - +
94B LEU* 1.3 82.2 - - + +
96B SER* 1.3 64.2 + - - +
99B ALA* 3.7 5.5 - - - +
100B LYS* 2.7 36.3 + - - +
136B HIS 5.1 0.4 - - - +
137B PHE* 6.0 0.4 - - + -
140B THR* 3.6 33.0 - - + +
143B LEU* 5.1 0.4 - - + -
88D PHE* 3.8 39.3 - - + -
136D HIS* 5.3 1.6 - - + +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ALA* 4.9 2.8 - - - +
145A PRO* 3.7 11.7 - - - -
148A SER* 5.1 1.3 - - - -
92B ASP* 2.6 46.7 + - - -
95B VAL* 1.3 80.3 - - - +
97B GLN* 1.3 60.2 + - - +
100B LYS* 3.9 13.4 + - - +
104B ARG* 3.5 14.2 + - - -
88D PHE* 4.2 3.6 - - - -
128D HIS* 2.9 35.4 + - - -
131D GLN* 5.3 0.2 + - - -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.4 12.8 - - - -
143A ALA* 3.3 18.7 - - - +
148A SER* 3.1 53.0 + - - +
149A HIS* 3.8 10.1 - - - +
152A PRO* 4.0 7.2 - - + -
68B LEU* 3.9 12.8 - - + +
92B ASP 3.5 0.4 + - - +
93B GLN* 3.2 24.5 + - - +
96B SER* 1.3 79.6 - - - +
98B VAL* 1.3 66.3 + - - +
100B LYS 4.2 0.2 - - - -
101B LEU* 3.2 27.0 + - - +
104B ARG* 2.8 29.1 + - - +
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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