Contacts of the strand formed by residues 172 - 177 (chain A) in PDB entry 4MYF
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 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A VAL* 3.2 25.6 - - + -
136A ASN* 4.1 4.3 - - + -
158A PHE* 3.7 37.0 - + + -
162A LEU* 3.9 33.9 - - + -
167A PHE* 3.7 19.3 - + + -
169A GLY 3.0 10.8 + - - +
170A LYS 3.4 0.4 - - - -
171A ARG* 1.3 79.3 - - - +
173A VAL* 1.3 69.5 + - - +
174A GLU* 3.3 44.2 - - + -
190A VAL* 4.1 13.5 - - + -
195A GLY* 3.6 2.1 - - - -
196A HIS* 3.0 31.0 + - - -
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Residues in contact with VAL 173 (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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134A VAL 2.9 8.1 + - - +
135A ILE* 3.3 10.0 - - + +
136A ASN* 2.8 27.9 + - - -
172A PHE* 1.3 84.2 - - - +
174A GLU* 1.3 77.7 + - - +
175A PHE* 4.3 5.2 - - + +
196A HIS* 3.5 7.6 - - + +
198A MET* 3.9 28.5 - - + -
215A ALA* 4.1 12.3 - - + +
218A LEU* 4.0 36.8 - - + -
219A THR* 4.0 11.9 - - + -
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Residues in contact with GLU 174 (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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136A ASN* 2.9 29.1 + - - +
138A ASP* 5.0 0.3 - - - +
140A HIS 4.1 1.7 - - - +
141A LEU* 2.7 53.6 - - + +
143A VAL* 4.0 1.7 - - - +
172A PHE* 3.3 34.9 - - + -
173A VAL* 1.3 70.3 - - - +
175A PHE* 1.3 56.1 + - - +
177A CYS* 3.8 7.0 - - + +
190A VAL* 3.8 10.3 - - + +
196A HIS 2.8 9.8 + - - +
197A LEU* 3.7 17.9 - - + -
198A MET* 2.8 34.0 + - - +
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Residues in contact with PHE 175 (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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135A ILE* 3.6 31.6 - - + -
136A ASN 2.8 13.4 + - - +
137A VAL* 3.4 7.6 - - + -
138A ASP 3.0 23.5 + - - +
173A VAL* 4.4 0.7 - - + -
174A GLU* 1.3 72.5 - - - +
176A ALA* 1.3 78.4 + - + +
177A CYS 3.2 1.9 + - - -
198A MET* 3.7 21.8 - - + -
203A VAL* 3.7 33.4 - - + -
208A ALA 3.8 6.5 - - - -
211A ALA* 3.6 13.5 - - + -
212A LEU* 3.5 36.8 - - + -
215A ALA* 4.0 0.9 - - + -
248A LEU* 4.9 0.2 - - + -
256A MET* 3.5 31.2 - - + -
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Residues in contact with ALA 176 (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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137A VAL* 4.8 1.8 - - + -
138A ASP 3.3 6.8 - - - +
139A SER* 3.6 9.4 + - - -
175A PHE* 1.3 91.4 - - + +
177A CYS* 1.3 63.9 + - - +
178A GLN* 4.0 7.4 + - - +
198A MET 2.7 16.5 + - - -
200A LEU* 3.9 21.4 - - + +
203A VAL* 3.9 4.1 - - + +
231A SER* 4.8 5.6 - - - +
248A LEU* 4.0 31.9 - - + -
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Residues in contact with CYS 177 (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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138A ASP 3.2 13.9 + - - +
139A SER 3.6 4.9 - - - +
140A HIS 4.9 0.7 - - - +
141A LEU* 4.0 22.4 - - + -
174A GLU* 3.8 24.0 - - + +
175A PHE 3.2 2.8 - - - -
176A ALA* 1.3 77.8 - - - +
178A GLN* 1.3 60.8 + - - +
182A CYS* 4.2 5.8 - - - -
197A LEU* 4.3 5.6 - - - -
198A MET 3.6 19.3 + - - -
199A TRP* 3.4 28.9 - - - -
200A LEU 2.9 23.9 + - - -
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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