Contacts of the helix formed by residues 162 - 175 (chain B) in PDB entry 5UNH
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 TYR 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ALA 2.8 29.6 + - - -
96A THR* 3.4 6.1 - - - +
98A PRO* 4.3 23.8 - - + -
99A LEU* 3.3 51.5 - - + +
112A PHE* 5.5 6.3 - + + -
116A MET* 5.2 1.6 - - + -
120A PHE* 3.8 12.3 - + - -
160B ALA 3.3 3.1 - - - +
161B SER* 1.3 81.3 + - - +
163B ILE* 1.4 74.6 + - + +
165B PRO* 3.3 16.3 - - + +
166B LEU* 3.4 43.7 + - + +
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Residues in contact with ILE 163 (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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116A MET* 3.8 35.9 - - + -
120A PHE* 4.5 10.3 - - + -
82B TYR* 3.4 40.8 - - + +
137B CYS* 3.8 20.6 - - - -
160B ALA* 4.1 17.6 - - - +
162B TYR* 1.4 87.1 - - + +
164B VAL* 1.3 66.2 + - - +
166B LEU* 3.0 9.0 + - + +
167B VAL* 2.9 29.3 + - + +
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Residues in contact with VAL 164 (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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81B ILE* 4.2 11.9 - - + -
82B TYR* 4.2 14.6 - - + -
85B ASN* 3.5 39.3 - - - +
134B PHE* 3.7 20.0 - - + -
160B ALA 3.8 15.9 + - - +
161B SER* 5.6 0.2 - - - -
163B ILE* 1.3 78.2 - - - +
165B PRO* 1.4 70.8 - - + +
167B VAL* 3.2 7.8 + - - +
168B TRP* 3.2 26.9 + - + -
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Residues in contact with PRO 165 (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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161B SER* 3.4 26.5 - - - +
162B TYR* 3.3 15.9 - - + +
164B VAL* 1.4 93.7 - - + +
166B LEU* 1.4 53.9 + - - +
168B TRP* 3.4 9.1 + - + +
169B CYS* 3.0 27.1 + - - +
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Residues in contact with LEU 166 (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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92A LEU* 5.0 7.2 - - + -
95A ALA* 4.2 22.9 - - + -
96A THR* 6.1 0.4 - - + -
120A PHE* 3.7 22.7 - - + -
123A PHE* 5.1 8.7 - - + -
162B TYR* 3.4 46.5 + - + +
163B ILE* 3.0 11.3 + - - +
165B PRO* 1.4 75.8 - - - +
167B VAL* 1.4 60.9 + - + +
169B CYS* 3.2 9.9 + - + +
170B MET* 2.9 58.5 + - + +
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Residues in contact with VAL 167 (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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130B ALA* 4.3 3.3 - - - +
133B PHE* 3.6 30.5 - - + +
134B PHE* 3.6 36.8 - - + -
137B CYS* 3.7 27.4 - - - -
163B ILE* 2.9 25.1 + - + +
164B VAL 3.2 6.9 + - - +
166B LEU* 1.4 74.9 - - - +
168B TRP* 1.3 57.9 + - - +
170B MET* 3.7 16.9 + - + -
171B ALA* 3.2 25.1 + - - +
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Residues in contact with TRP 168 (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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85B ASN* 3.0 38.4 - - - +
88B VAL* 4.8 10.5 - - + -
89B ALA* 3.9 11.7 - - + -
92B LEU* 5.2 2.5 - - + -
126B LEU* 3.8 21.1 - - + -
127B ASN* 3.6 26.0 - - - -
130B ALA* 3.6 24.9 - - + -
134B PHE* 3.4 19.7 - + - -
164B VAL* 3.2 32.2 + - + -
165B PRO* 3.8 9.4 - - + +
166B LEU 3.2 0.4 - - - -
167B VAL* 1.3 75.1 - - - +
169B CYS* 1.4 58.7 + - - +
171B ALA* 3.3 3.5 + - + +
172B CYS* 3.0 36.6 + - - -
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Residues in contact with CYS 169 (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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59A PHE* 3.6 34.8 - - + -
91A LEU* 5.2 1.1 - - - -
92A LEU* 5.5 4.9 - - - -
95A ALA* 5.8 0.4 - - - -
165B PRO 3.0 18.1 + - - +
166B LEU* 3.2 15.9 + - + +
168B TRP* 1.4 75.7 - - - +
170B MET* 1.4 55.9 + - - +
172B CYS* 3.2 8.1 + - - +
173B LEU* 3.1 52.0 + - - +
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Residues in contact with MET 170 (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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92A LEU* 4.0 22.9 - - + -
123A PHE* 4.5 22.0 - - + -
133B PHE* 3.8 22.7 - - + -
166B LEU* 2.9 46.6 + - + +
167B VAL* 3.8 18.2 - - + +
168B TRP 3.4 0.2 - - - -
169B CYS* 1.4 75.3 - - - +
171B ALA* 1.4 54.3 + - - +
173B LEU* 3.6 6.7 + - - +
174B SER* 2.8 36.7 + - - -
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Residues in contact with ALA 171 (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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126B LEU* 3.3 33.1 - - + +
129B PHE* 4.2 6.8 - - + -
130B ALA* 3.9 18.2 - - + +
133B PHE* 3.9 6.9 - - + -
167B VAL 3.2 18.2 + - - +
168B TRP* 3.5 7.2 - - - +
169B CYS 3.3 0.2 - - - -
170B MET* 1.4 74.6 - - - +
172B CYS* 1.4 61.1 + - - +
174B SER* 3.6 2.1 + - - -
175B SER* 3.0 27.0 + - - -
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Residues in contact with CYS 172 (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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126B LEU* 3.5 26.0 - - - -
168B TRP* 3.0 23.1 + - - +
169B CYS* 3.5 12.8 - - - +
171B ALA* 1.4 75.7 - - - +
173B LEU* 1.3 62.0 + - + +
175B SER* 3.1 17.5 + - - -
176B LEU* 3.5 16.9 - - - +
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Residues in contact with LEU 173 (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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66A VAL* 6.1 0.9 - - + -
84A PHE* 4.0 10.0 - - - -
88A VAL* 3.8 45.4 - - + +
91A LEU* 3.8 28.0 - - + -
92A LEU* 4.0 23.6 - - + -
169B CYS* 3.1 35.4 + - - +
170B MET* 3.8 6.1 - - - +
172B CYS* 1.3 79.6 - - + +
174B SER* 1.3 61.1 + - - +
175B SER 3.2 0.7 - - - -
176B LEU* 3.4 32.0 + - + +
177B PRO* 4.1 0.9 - - - +
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Residues in contact with SER 174 (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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129B PHE* 3.6 41.2 - - - -
133B PHE* 3.8 12.8 - - - -
170B MET 2.8 22.3 + - - -
171B ALA 4.0 1.8 - - - -
172B CYS 3.5 0.4 - - - -
173B LEU* 1.3 75.5 - - - +
175B SER* 1.4 57.5 + - - +
176B LEU 3.5 0.4 - - - -
177B PRO* 3.6 12.9 - - - +
218B LEU* 4.1 20.5 - - - +
1501B 8EM 3.8 10.0 - - - -
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Residues in contact with SER 175 (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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122B SER* 3.9 11.7 + - - -
125B THR* 3.7 25.4 - - - -
126B LEU* 3.8 18.1 - - - +
171B ALA 3.0 18.7 + - - -
172B CYS* 3.1 12.5 + - - -
173B LEU 3.2 0.2 - - - -
174B SER* 1.4 75.2 - - - +
176B LEU* 1.4 62.0 + - - +
177B PRO* 3.6 2.0 - - - -
178B THR* 3.4 12.1 - - - -
179B PHE* 3.3 18.7 + - - +
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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