Contacts of the strand formed by residues 162 - 166 (chain A) in PDB entry 1YI1
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 GLY 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ALA* 3.5 25.1 - - - -
154A TYR* 4.5 6.1 - - - -
155A ALA* 3.8 2.3 - - - +
160A LYS 3.8 0.8 + - - -
161A PRO* 1.3 72.0 - - - +
163A ILE* 1.3 67.0 + - - +
188A PRO 3.1 12.1 + - - -
189A LEU* 3.5 12.0 - - - +
190A VAL 2.8 26.7 + - - +
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Residues in contact with ILE 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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107A LEU* 4.6 11.4 - - + -
112A VAL* 3.9 16.4 - - + -
114A THR 4.2 6.8 + - - +
115A VAL* 3.4 30.3 - - + -
116A PHE* 3.0 29.5 + - - -
151A ALA* 4.1 4.8 - - - +
154A TYR* 5.5 1.0 - - + -
161A PRO* 3.4 19.5 - - + +
162A GLY* 1.3 81.8 - - - +
164A CYS* 1.3 62.8 + - - +
165A ILE* 4.3 14.6 - - + -
190A VAL* 3.3 13.7 - - + +
192A ILE* 4.9 4.0 - - + -
239A PHE* 3.8 36.1 - - + -
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Residues in contact with CYS 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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116A PHE 3.2 10.8 - - - +
147A GLY* 4.1 11.7 - - - +
148A VAL* 3.4 32.3 - - - +
151A ALA* 4.1 14.6 - - + -
162A GLY 4.2 0.6 - - - -
163A ILE* 1.3 74.0 - - - +
165A ILE* 1.3 66.3 + - - +
175A LEU* 4.0 11.2 - - + -
189A LEU* 5.1 4.3 - - - -
190A VAL 3.2 7.4 + - - +
191A ALA* 3.3 23.1 - - - +
192A ILE 3.0 22.0 + - - +
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Residues in contact with ILE 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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107A LEU* 4.6 11.4 - - + -
115A VAL* 4.5 12.8 - - + -
116A PHE 3.0 7.4 + - - +
117A ALA* 3.3 17.0 - - + -
118A TYR* 3.2 24.3 + - - +
123A SER* 5.1 4.3 - - - -
126A ILE* 4.3 24.2 - - + -
127A HIS* 5.0 5.8 - - - +
130A LEU* 4.2 24.0 - - + -
163A ILE* 4.3 7.6 - - + -
164A CYS* 1.3 81.4 - - - +
166A ALA* 1.3 70.9 + - - +
175A LEU* 5.5 1.1 - - - -
192A ILE* 3.2 38.4 - - + +
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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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118A TYR 4.2 6.1 - - - -
123A SER* 4.0 10.5 - - - -
144A GLU* 3.8 11.4 - - + +
165A ILE* 1.3 76.5 - - - +
167A THR* 1.3 62.2 + - - +
171A GLY 3.7 19.1 - - - +
175A LEU* 3.7 30.9 - - + +
192A ILE 2.8 7.4 + - - +
193A THR* 3.1 5.4 - - + -
194A GLY 2.9 21.1 + - - -
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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