Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 1Y8Q
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 LYS 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ASP 3.1 17.6 + - - +
128A ALA* 3.3 5.1 - - + -
129A VAL* 2.9 26.7 + - - +
150A SER 4.2 5.1 + - - +
151A ILE* 1.3 75.1 - - - +
153A PHE* 1.3 58.2 + - - +
154A PHE* 3.8 19.7 - - + -
168A ASN 4.1 4.3 - - - -
169A LEU* 3.9 35.0 - - + +
171A GLU 6.0 0.7 - - - -
172A HIS* 3.7 20.1 + - - +
317A ALA* 3.6 27.1 + - + -
318A LEU* 4.8 8.4 + - + +
320A GLN* 5.0 8.1 - - - +
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Residues in contact with PHE 153 (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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129A VAL 3.7 5.6 - - - -
131A LEU* 3.8 24.5 - - + -
139A ILE* 3.6 23.3 - - + -
142A VAL* 3.8 18.4 - - + -
143A ASP* 3.2 43.7 - - + +
146A CYS* 4.1 15.5 - - + -
151A ILE 3.4 0.8 + - - +
152A LYS* 1.3 74.1 - - - +
154A PHE* 1.3 80.3 + - - +
155A THR* 3.9 18.4 - - + -
166A PHE* 4.0 26.5 - + - -
167A ALA* 3.3 3.6 - - - +
168A ASN* 2.9 41.6 + - + +
216A VAL* 4.5 0.2 - - + -
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Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 4.2 10.5 - - + -
129A VAL 2.8 18.0 + - - +
130A CYS* 4.1 7.9 - - - -
131A LEU 2.9 22.0 + - - -
152A LYS* 3.8 23.8 - - + -
153A PHE* 1.3 85.8 - - - +
155A THR* 1.3 63.4 + - - +
166A PHE 3.3 6.7 - - - +
167A ALA* 3.8 25.6 - - + -
169A LEU* 3.4 20.0 - - + -
310A LEU* 3.8 22.4 - - + -
313A GLU* 3.8 23.6 - - + -
314A ILE* 3.7 27.4 - - + -
317A ALA* 3.7 16.6 - - + -
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Residues in contact with THR 155 (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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130A CYS* 5.0 0.4 - - - -
131A LEU* 3.3 16.0 + - - +
139A ILE* 3.8 24.9 - - + +
153A PHE* 3.9 15.9 - - + -
154A PHE* 1.3 76.4 - - - +
156A GLY* 1.3 60.8 + - - +
157A ASP* 4.7 1.7 + - - -
164A TYR* 3.4 18.9 + - + +
165A THR* 3.3 4.0 - - - -
166A PHE* 2.8 61.6 + - + +
216A VAL* 4.9 1.1 - - + -
310A LEU* 4.2 6.0 - - - +
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Residues in contact with GLY 156 (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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47A LEU* 3.4 13.4 - - - +
131A LEU 3.0 14.2 + - - +
132A THR* 3.6 2.9 - - - -
155A THR* 1.3 79.3 + - - +
157A ASP* 1.3 77.6 + - - +
164A TYR* 3.1 18.8 - - - -
310A LEU* 4.0 13.5 - - - +
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Residues in contact with ASP 157 (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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47A LEU* 3.5 7.0 - - - +
132A THR* 4.0 3.8 - - - +
133A CYS* 2.7 32.7 + - - -
134A CYS 4.5 1.6 + - - +
139A ILE* 4.9 2.3 - - - +
155A THR* 4.7 2.6 + - - -
156A GLY* 1.3 83.0 - - - +
158A VAL* 1.3 67.0 + - - +
159A PHE* 3.3 23.9 - - + -
163A GLY* 3.3 2.6 - - - -
164A TYR* 3.0 49.7 + - + +
247A LEU* 5.5 1.2 - - - +
250A ARG* 3.0 30.7 + - - +
306A VAL* 4.3 0.9 - - - +
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Residues in contact with VAL 158 (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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47A LEU* 4.2 16.2 - - + +
157A ASP* 1.3 80.2 + - - +
159A PHE* 1.3 74.7 + - - +
160A GLY 3.9 8.3 - - - +
162A HIS 3.4 12.3 - - - +
250A ARG* 5.6 0.9 + - - -
297A SER 4.2 4.5 - - - +
298A GLU* 4.6 17.1 + - + +
299A MET 4.5 7.2 - - - +
302A VAL* 3.6 28.5 - - + +
303A CYS* 4.0 34.3 - - - -
306A VAL* 4.1 13.5 - - + -
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Residues in contact with PHE 159 (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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157A ASP* 3.3 25.4 - - + -
158A VAL* 1.3 79.7 - - - +
160A GLY* 1.3 64.7 + - - +
161A TYR 3.2 0.5 + - - -
162A HIS* 2.9 29.1 + - + +
163A GLY* 5.4 2.7 - - - -
164A TYR* 4.5 13.9 - + - -
243A LEU* 4.9 6.1 - - + -
246A LEU* 3.3 56.5 - - + -
247A LEU* 5.4 2.9 - - + -
250A ARG* 3.3 32.3 - - - -
256A ASP* 3.7 22.9 - - + -
257A PRO* 5.0 1.1 - - + -
294A TYR 3.6 0.2 - - - +
295A CYS* 3.3 23.1 - - + +
296A PHE 5.3 0.2 - - - -
297A SER 3.9 2.7 - - - +
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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