Contacts of the helix formed by residues 158 - 169 (chain A) in PDB entry 3U44
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 GLU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLU* 4.4 11.3 + - - +
156A LYS* 2.9 51.2 + - + +
157A GLY* 1.3 75.6 - - - +
159A LYS* 1.3 66.8 + - + +
160A ALA* 4.6 9.3 - - + +
161A PHE* 3.4 22.0 + - + +
162A PHE* 3.0 17.7 - - - -
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLY 3.4 3.7 + - - -
158A GLU* 1.3 72.3 - - + +
160A ALA* 1.3 76.7 + - + +
162A PHE* 3.1 21.0 + - - +
163A GLU* 3.3 16.5 + - + +
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Residues in contact with ALA 160 (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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158A GLU* 3.4 9.1 - - + +
159A LYS* 1.3 86.8 - - + +
161A PHE* 1.3 63.5 + - - +
163A GLU* 3.2 12.9 + - - +
164A LEU* 3.2 16.5 + - - +
340A PRO 5.5 0.2 - - - +
341A VAL* 6.0 0.7 - - - -
344A THR* 3.3 31.4 + - + +
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Residues in contact with PHE 161 (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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150A PHE* 4.3 11.9 - + - -
153A GLU* 3.4 55.4 - - + +
154A TYR* 3.4 38.8 - + - -
158A GLU* 3.4 21.4 + - + +
159A LYS 3.1 0.6 + - - -
160A ALA* 1.3 78.2 - - - +
162A PHE* 1.3 75.1 + + - +
164A LEU* 3.0 11.7 + - + +
165A VAL* 3.0 41.9 + - + +
177A LEU* 4.4 11.2 - - + -
344A THR* 4.0 11.6 - - + +
348A LEU* 4.4 18.2 - - + -
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Residues in contact with PHE 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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154A TYR* 3.9 27.8 - + - -
157A GLY* 3.3 43.3 - - - -
158A GLU 3.0 18.6 - - - -
159A LYS* 3.1 8.8 + - - +
161A PHE* 1.3 83.8 - + - +
163A GLU* 1.3 61.3 + - - +
165A VAL* 4.1 4.5 - - + -
166A ASP* 2.8 40.9 + - - +
883B TYR* 5.0 8.5 - + - -
884B TYR* 3.1 44.8 + + + +
887B GLU* 5.7 0.7 - - - -
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Residues in contact with GLU 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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159A LYS* 3.3 17.4 + - + +
160A ALA* 3.4 10.8 - - - +
161A PHE 3.2 0.4 - - - -
162A PHE* 1.3 79.3 - - - +
164A LEU* 1.3 57.5 + - - +
166A ASP* 4.2 8.0 - - - +
167A ARG* 3.1 60.3 + - - +
341A VAL* 5.0 5.4 - - + -
837A PRO* 4.6 1.0 - - - +
838A GLN* 3.9 24.9 + - - +
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Residues in contact with LEU 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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160A ALA 3.2 10.2 + - - +
161A PHE* 3.0 12.8 + - + +
163A GLU* 1.3 76.3 - - - +
165A VAL* 1.3 63.8 + - - +
167A ARG* 3.4 3.6 + - - +
168A TYR* 3.1 54.4 + - + +
177A LEU* 4.0 12.5 - - + +
341A VAL* 3.7 17.4 - - + +
344A THR* 4.0 15.5 - - + -
345A LEU* 3.6 44.2 - - + +
348A LEU* 4.0 22.7 - - + -
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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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154A TYR* 3.8 19.7 - - + +
161A PHE* 3.0 45.9 + - + +
162A PHE* 3.7 5.2 - - - +
164A LEU* 1.3 72.1 - - + +
166A ASP* 1.3 65.3 + - - +
167A ARG 2.8 5.6 + - - -
168A TYR 3.1 0.3 + - - -
169A THR* 2.9 46.7 + - + +
174A ASP* 4.8 2.7 - - + -
177A LEU* 3.5 26.0 - - + -
884B TYR* 3.9 17.9 - - + +
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Residues in contact with ASP 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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162A PHE* 2.8 23.6 + - - +
163A GLU* 4.2 9.7 - - - +
165A VAL* 1.3 72.9 - - - +
167A ARG* 1.3 59.6 + - - +
169A THR 3.9 3.8 - - - +
171A ASP* 3.6 37.5 - - - +
837A PRO* 4.1 24.7 - - + +
838A GLN* 5.4 2.0 + - - -
840A ARG* 5.1 2.8 + - - -
884B TYR* 2.7 29.6 + - - -
887B GLU* 5.4 0.9 - - - +
888B LYS* 4.4 1.7 + - - +
891B LYS* 3.7 28.1 + - - -
1015B MET* 5.5 3.5 - - - +
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Residues in contact with ARG 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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163A GLU* 3.1 53.6 + - - +
164A LEU* 3.5 5.2 - - - +
165A VAL 2.8 2.6 + - - -
166A ASP* 1.3 81.2 - - - +
168A TYR* 1.3 65.2 + - + +
169A THR 3.6 1.5 - - - +
337A GLU 5.8 0.8 + - - -
338A MET* 3.8 28.6 - - - -
341A VAL* 3.4 26.4 - - - +
834A TYR* 6.2 0.6 - - - -
835A ILE* 2.7 78.1 + - + +
836A HIS* 4.4 4.2 + - - +
837A PRO* 3.7 21.7 - - + +
838A GLN* 5.2 0.2 + - - -
1015B MET* 5.4 1.7 - - - +
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Residues in contact with TYR 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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164A LEU* 3.1 45.1 + - + +
165A VAL 3.1 2.2 + - - -
167A ARG* 1.3 85.6 - - + +
169A THR* 1.3 60.5 + - - +
170A THR 4.1 0.3 + - - -
176A ASP* 3.7 15.5 - - - +
177A LEU* 4.2 16.6 - - + -
180A LEU* 4.0 18.8 - - + -
338A MET* 4.1 7.6 - - + +
341A VAL* 4.0 13.2 - - + -
342A ILE* 4.4 2.3 - - + +
345A LEU* 4.9 3.8 - - + -
821A SER* 4.7 4.9 - - - -
822A TYR* 4.5 22.7 - + + -
830A PHE* 3.6 12.7 - + - -
832A THR* 2.6 46.9 + - - +
835A ILE* 4.4 12.3 - - + -
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Residues in contact with THR 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 44.8 + - + +
166A ASP 3.9 5.9 - - - +
167A ARG 4.8 1.3 - - - +
168A TYR* 1.3 80.2 - - - +
170A THR* 1.3 57.2 + - - +
171A ASP* 2.9 15.7 + - - +
173A HIS 2.7 23.7 + - - +
174A ASP* 2.9 25.1 + - - -
176A ASP* 3.6 7.3 + - - -
177A LEU* 4.2 7.6 - - - -
888B LYS* 3.6 20.4 - - - +
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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