Contacts of the helix formed by residues 161 - 172 (chain A) in PDB entry 6UPR
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 LYS 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.6 26.5 + - - -
154A SER* 5.2 15.3 - - - -
157A GLY* 5.9 2.7 - - - -
159A GLY 3.7 6.5 + - - +
160A LEU* 1.3 75.7 - - - +
162A PRO* 1.3 73.6 - - + +
163A LEU* 3.1 8.1 - - + +
164A ASP* 2.8 33.5 + - - +
165A VAL* 3.2 11.6 + - - +
52B GLU* 4.0 23.4 + - - +
53B THR 5.7 1.6 + - - +
76B HIS* 3.8 27.8 - - + +
77B HIS* 4.8 0.7 - - - -
108B GLY 3.9 18.5 + - - -
109B ASP* 4.2 12.8 + - - +
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Residues in contact with PRO 162 (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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161A LYS* 1.3 83.5 - - + +
163A LEU* 1.3 55.9 + - - +
165A VAL* 3.3 4.6 + - + +
166A ALA* 3.0 31.4 + - - +
76B HIS* 3.2 31.4 - - + +
77B HIS* 3.7 24.5 - - + +
109B ASP 3.3 20.2 - - - +
110B GLN* 5.2 1.6 - - - -
111B ILE* 3.9 20.0 - - + +
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Residues in contact with LEU 163 (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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45A GLU* 5.5 8.7 - - + +
105A TYR* 3.7 25.5 + - + +
106A GLY* 4.2 22.4 - - - +
111A CYS* 4.8 1.6 - - + -
114A CYS* 4.3 9.4 - - - -
115A PHE* 3.7 26.2 - - + -
151A TYR* 4.2 1.1 - - - +
161A LYS* 3.1 6.1 + - + +
162A PRO* 1.3 79.5 - - - +
164A ASP* 1.3 64.7 + - - +
166A ALA* 4.6 0.2 - - - -
167A PHE* 3.1 24.6 + - - +
109B ASP 5.1 0.8 + - - -
111B ILE* 3.9 34.9 - - + +
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Residues in contact with ASP 164 (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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45A GLU* 6.1 0.7 - - - +
151A TYR* 2.4 47.8 + - + +
152A PHE 5.1 0.5 - - - +
153A ILE* 4.6 9.0 - - - +
154A SER 5.4 1.2 + - - -
159A GLY 4.5 1.2 - - - +
160A LEU* 3.8 23.4 - - + +
161A LYS* 2.8 41.9 + - - +
163A LEU* 1.3 80.5 - - - +
165A VAL* 1.3 60.6 + - - +
167A PHE* 4.0 0.9 - - - +
168A MET* 3.0 32.9 + - + +
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Residues in contact with VAL 165 (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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160A LEU* 4.1 24.9 - - + -
161A LYS 3.2 12.4 + - - +
162A PRO* 3.3 6.9 + - + +
164A ASP* 1.3 72.9 - - - +
166A ALA* 1.3 67.2 + - - +
168A MET* 3.4 0.5 + - - +
169A LYS* 2.9 36.2 + - + +
206A HIS* 3.6 55.0 - - + +
208A ILE* 4.2 9.9 - - + -
77B HIS* 4.8 6.7 - - + -
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Residues in contact with ALA 166 (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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115A PHE* 3.7 16.7 - - + -
162A PRO 3.0 17.7 + - - +
163A LEU 4.1 1.8 - - - +
165A VAL* 1.3 78.1 - - - +
167A PHE* 1.3 62.6 + - - +
169A LYS* 3.7 5.0 + - - +
170A ALA* 3.1 23.2 + - - +
111B ILE* 4.1 17.5 - - + -
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Residues in contact with PHE 167 (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 VAL* 3.6 34.1 - - + -
105A TYR* 3.5 13.5 - + - +
115A PHE* 3.5 36.3 - + + -
118A ILE* 3.7 34.8 - - + -
149A CYS* 4.4 1.6 - - - -
151A TYR* 3.3 27.6 - + + -
163A LEU 3.1 18.3 + - - +
164A ASP 4.1 1.8 - - - +
166A ALA* 1.3 75.2 - - - +
168A MET* 1.3 64.2 + - + +
170A ALA* 2.9 19.1 + - + +
171A ILE* 3.2 48.4 + - + +
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Residues in contact with MET 168 (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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151A TYR* 4.5 25.8 - - + -
153A ILE* 5.1 1.6 - - + -
160A LEU* 3.9 28.3 - - + -
164A ASP* 3.0 29.5 + - + +
167A PHE* 1.3 77.8 - - + +
169A LYS* 1.3 56.8 + - - +
170A ALA 3.2 0.2 + - - -
171A ILE* 3.2 1.7 + - - -
172A HIS* 2.9 36.4 + - - +
177A ILE* 3.4 36.6 - - + +
179A PRO* 5.2 5.6 - - - -
203A ILE* 5.0 6.7 - - + -
208A ILE* 3.8 40.6 - - + -
210A ILE* 4.9 4.0 - - - -
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Residues in contact with LYS 169 (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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165A VAL* 2.9 35.8 + - + +
166A ALA* 3.9 5.6 - - - +
168A MET* 1.3 76.3 - - - +
170A ALA* 1.3 57.7 + - - +
171A ILE 3.3 0.2 - - - -
172A HIS* 3.0 35.3 + - + +
173A ASN* 5.3 0.9 + - - -
206A HIS* 2.9 28.3 + - + +
207A ASN* 3.9 12.5 + - - +
208A ILE* 3.8 16.2 - - + -
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Residues in contact with ALA 170 (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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115A PHE* 4.2 12.6 - - + -
119A ILE* 3.7 28.4 - - + +
166A ALA 3.1 18.2 + - - +
167A PHE* 2.9 12.4 + - + +
169A LYS* 1.3 78.5 - - - +
171A ILE* 1.3 64.0 + - + +
172A HIS 3.8 0.2 - - - -
173A ASN 5.5 0.2 - - - -
174A LYS* 4.4 9.9 - - - +
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Residues in contact with ILE 171 (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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41A MET* 5.7 0.2 - - - -
118A ILE* 4.9 0.2 - - + -
119A ILE* 3.9 19.7 - - + -
122A ILE* 4.0 20.2 - - + -
149A CYS* 4.0 12.1 - - - -
167A PHE* 3.4 52.5 - - + +
168A MET 3.9 3.1 - - - +
170A ALA* 1.3 83.3 - - + +
172A HIS* 1.3 63.3 + - - +
173A ASN 3.1 3.4 - - - -
174A LYS* 2.8 27.2 + - + -
175A VAL* 3.0 38.4 + - + +
177A ILE* 3.9 13.0 - - + -
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Residues in contact with HIS 172 (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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168A MET 2.9 15.3 + - - +
169A LYS* 3.0 44.8 + - - +
171A ILE* 1.3 77.6 - - - +
173A ASN* 1.3 75.7 + - - +
174A LYS 3.4 1.5 + - - -
175A VAL 3.9 10.4 - - - +
177A ILE* 3.7 10.3 - - + -
207A ASN 3.3 22.2 - - - -
208A ILE* 3.7 3.4 - - + -
209A LYS* 2.9 70.0 + - + +
295A HIS* 4.2 8.0 - - - -
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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