Contacts of the helix formed by residues 165 - 170 (chain A) in PDB entry 1U3W
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 PRO 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA 3.7 3.3 - - - +
164A SER* 1.3 85.7 - - - +
166A LEU* 1.3 59.8 + - - +
167A GLU* 3.2 24.0 - - - +
168A LYS* 3.1 18.1 + - + -
169A VAL* 3.0 22.2 + - - +
335A PHE* 3.7 31.0 - - + -
336A MET* 3.9 7.2 - - + -
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Residues in contact with LEU 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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41A VAL* 3.8 41.3 - - + -
42A ALA* 3.4 12.9 - - + +
70A ALA* 3.8 15.3 - - + +
71A GLY 3.9 22.4 - - - +
72A ILE* 4.3 3.8 - - + -
88A LYS* 3.7 38.1 - - + -
89A VAL 5.2 0.2 - - - +
160A ILE* 3.8 24.7 - - + -
164A SER 3.3 8.0 + - - +
165A PRO* 1.3 71.8 - - - +
167A GLU* 1.3 64.5 + - - +
168A LYS 3.1 1.7 + - - -
169A VAL* 3.9 4.7 - - + -
170A CYS* 3.3 18.9 + - - +
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Residues in contact with GLU 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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41A VAL* 5.2 2.3 - - + +
42A ALA* 3.6 16.1 - - + +
165A PRO* 3.5 18.8 - - - +
166A LEU* 1.3 88.2 + - - +
168A LYS* 1.3 80.7 + - + +
170A CYS* 4.1 2.7 - - - -
346A ILE* 3.7 12.8 - - - +
349A VAL* 6.2 5.4 - - + -
371A VAL* 3.6 22.8 - - + +
373A THR* 5.2 11.4 - - + -
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Residues in contact with LYS 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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165A PRO* 3.1 21.1 + - + +
167A GLU* 1.3 104.6 + - + +
169A VAL* 1.3 63.1 + - - +
170A CYS* 3.2 5.8 + - - -
171A LEU* 3.2 18.7 + - - +
335A PHE* 4.1 22.9 - - + -
342A LEU* 3.3 17.2 - - + +
343A ASP* 3.4 28.9 + - - +
346A ILE* 3.8 19.0 - - + +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 4.7 0.7 - - + -
90A ILE* 3.4 9.0 - - + +
160A ILE* 3.9 27.1 - - + -
164A SER* 4.1 12.3 - - - +
165A PRO 3.0 15.1 + - - +
166A LEU* 3.9 13.5 - - + -
168A LYS* 1.3 71.9 - - - +
170A CYS* 1.3 61.6 + - - +
171A LEU 3.0 2.0 - - - -
172A ILE* 2.8 38.4 + - + +
332A VAL* 4.4 7.2 - - + -
335A PHE* 3.5 41.1 - - + -
342A LEU* 4.1 6.1 - - - -
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Residues in contact with CYS 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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42A ALA* 4.0 4.9 - - - +
44A GLY 4.4 7.6 - - - -
68A GLU* 3.4 13.2 - - - +
69A ALA* 3.6 37.5 + - - +
70A ALA* 3.7 4.2 - - - +
90A ILE* 4.8 0.2 - - - -
166A LEU 3.3 20.7 + - - +
167A GLU 3.9 7.9 - - - -
168A LYS 3.2 1.2 - - - -
169A VAL* 1.3 78.9 - - - +
171A LEU* 1.3 63.9 + - - +
173A GLY* 2.8 21.2 + - - +
371A VAL* 3.9 35.4 - - - -
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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