Contacts of the strand formed by residues 164 - 168 (chain A) in PDB entry 1SHC
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 VAL 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 4.8 8.1 - - + -
124A LEU* 6.1 3.1 - - + -
154A SER 4.4 2.7 - - - +
155A GLY* 4.1 15.5 - - - +
160A THR* 4.9 0.7 - - - -
162A GLU 5.4 0.4 - - - +
163A TYR* 1.3 83.9 - - - +
165A ALA* 1.3 61.7 + - - +
166A TYR* 5.9 0.7 - - + -
179A ILE* 4.0 1.4 - - - +
180A LEU* 3.0 58.1 + - + +
181A GLU* 5.2 0.7 - - - -
183A PRO* 5.0 14.1 - - + -
186A LEU* 5.5 0.4 - - + -
187A ALA* 4.9 5.8 - - - +
190A VAL* 3.8 33.9 - - + -
191A ILE* 5.2 2.5 - - + -
194A ILE* 5.6 5.6 - - + -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 5.0 1.6 + - - +
78A THR* 5.2 0.9 - - + -
82A ILE* 4.6 16.6 - - + -
153A ALA 4.0 0.2 - - - -
154A SER* 2.6 38.1 + - - +
155A GLY* 4.1 1.8 - - - -
159A ASP* 3.4 22.6 - - + +
160A THR* 5.0 4.2 + - + -
164A VAL* 1.3 76.5 - - - +
166A TYR* 1.3 61.7 + - - +
167A VAL* 5.8 2.0 - - + -
177A CYS* 5.1 5.6 - - - -
178A HIS 3.2 10.5 - - - +
179A ILE* 4.8 6.3 - - + -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 4.7 0.3 - - - -
122A ILE* 5.4 0.3 - - - +
124A LEU* 5.7 3.8 - - + -
131A LEU* 6.2 6.1 - - + -
133A LEU* 3.3 28.3 - - + +
142A ILE* 5.7 0.9 - - - +
146A HIS* 6.0 6.3 - + + -
150A ILE* 4.7 11.9 - - + -
152A PHE 3.3 4.9 - - - -
153A ALA* 3.7 22.9 - - + +
154A SER 4.4 1.6 - - - +
164A VAL* 5.9 0.7 - - + -
165A ALA* 1.3 76.9 - - - +
167A VAL* 1.3 61.8 + - - +
168A ALA* 3.3 17.2 + - + -
178A HIS* 2.9 63.0 + + + +
180A LEU* 3.3 32.5 - - + +
194A ILE* 5.8 9.4 - - + -
198A PHE* 6.5 0.4 - + - -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 5.6 3.1 - - + -
66A MET* 4.4 4.7 - - + -
74A ARG* 5.4 10.1 - - - +
150A ILE* 3.5 2.5 - - - +
151A SER* 3.0 21.2 + - - +
152A PHE* 2.8 52.5 + - + +
165A ALA* 5.8 1.6 - - + -
166A TYR* 1.3 72.2 - - - +
168A ALA* 1.3 59.5 + - - +
175A ARG* 4.3 10.5 - - + -
176A ALA 3.2 13.2 - - - +
177A CYS* 3.5 30.1 - - + +
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Residues in contact with ALA 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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146A HIS* 5.0 15.9 - - + +
150A ILE* 3.7 17.5 - - + -
151A SER* 3.4 5.1 + - - -
166A TYR* 3.3 18.7 + - + +
167A VAL* 1.3 74.2 - - - +
169A LYS* 1.3 76.3 + - - +
176A ALA* 3.1 27.5 + - + +
178A HIS* 4.7 12.1 - - + +
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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