Contacts of the strand formed by residues 166 - 170 (chain A) in PDB entry 3S8W
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 PHE 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL 3.9 0.3 - - - +
124A MSE 3.8 0.9 - - - -
125A VAL* 3.2 70.7 + - + +
127A PHE* 5.3 7.6 - - + -
141A LEU* 3.9 22.0 - - + -
156A PRO* 3.9 23.1 - - + -
157A GLU 5.6 6.3 - - - +
158A ILE* 5.3 13.0 - - + -
165A ASN* 1.3 78.1 - - - +
167A THR* 1.3 74.1 + - - +
168A TYR* 4.1 11.2 - - + -
1C CL 4.3 4.9 - - - -
155C LYS 6.0 1.3 - - - +
157C GLU* 5.7 2.9 - - + -
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 4.5 3.8 - - + -
123A VAL 3.3 12.3 - - - +
124A MSE 3.4 32.2 - - - +
166A PHE* 1.3 80.2 - - - +
168A TYR* 1.3 64.3 + - - +
169A ILE* 4.2 18.8 - - + -
1C CL 3.6 9.3 - - - +
155C LYS 4.8 0.4 + - - +
156C PRO* 3.4 7.2 - - + +
157C GLU* 3.0 25.1 + - - +
168C TYR* 4.2 31.8 + - + -
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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
----------------------------------------------------------
123A VAL* 2.7 46.8 + - - +
143A ILE* 3.8 28.0 - - + -
154A HIS* 3.6 24.3 - + + +
155A LYS 4.7 2.9 + - - -
156A PRO* 3.7 17.5 - - + -
166A PHE* 4.1 10.2 - - + -
167A THR* 1.3 74.8 - - - +
169A ILE* 1.3 68.3 - - - +
170A ILE* 3.9 22.4 - - + -
157C GLU* 3.5 49.1 - - + -
159C LYS* 3.0 37.5 - - + +
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Residues in contact with ILE 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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120A HIS* 4.1 19.7 - - + +
121A ILE 3.5 4.9 - - - +
122A ASN* 3.8 37.5 - - - +
167A THR* 4.2 8.7 - - + -
168A TYR* 1.3 77.4 - - - +
170A ILE* 1.3 63.6 + - - +
171A ASP 3.6 1.2 + - - -
141C LEU* 6.4 0.9 - - + -
156C PRO* 4.2 19.7 - - + -
157C GLU 2.8 17.5 + - - +
158C ILE* 4.1 20.0 - - + +
159C LYS* 3.2 26.7 + - - +
166C PHE* 4.2 18.8 - - + -
167C THR 4.5 5.8 - - - +
168C TYR* 4.7 6.1 - - + -
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Residues in contact with ILE 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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120A HIS* 3.0 5.4 - - - +
121A ILE* 2.7 46.8 + - + +
123A VAL* 3.9 22.7 - - + -
143A ILE* 4.1 15.9 - - + -
145A GLU* 3.4 42.0 - - + +
154A HIS* 4.1 8.7 - - + +
168A TYR* 3.9 21.1 - - + -
169A ILE* 1.3 69.9 - - - +
171A ASP* 1.3 62.1 + - - +
173A LEU* 3.8 19.8 - - + +
181A VAL* 4.3 11.4 - - + -
159C LYS* 4.4 7.2 - - - +
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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