Contacts of the strand formed by residues 148 - 153 (chain A) in PDB entry 2UYC
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 HIS 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A SER* 3.6 26.1 + - - -
147A PHE* 1.3 77.4 + - - +
149A ALA* 1.3 61.0 + - - +
167A TYR 3.5 1.0 - - - +
168A MET* 3.2 2.9 - - - -
169A ILE 2.8 48.3 + - - +
171A PHE* 3.9 16.6 - + - -
177A ILE 4.9 8.6 + - - -
178A GLN* 6.3 2.0 - - - -
180A PHE* 3.9 35.4 + + + +
182A PHE* 3.6 20.0 - - + -
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Residues in contact with ALA 149 (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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133A LEU* 4.4 10.8 - - + -
147A PHE* 3.5 32.7 + - + -
148A HIS* 1.3 75.2 - - - +
150A LYS* 1.3 63.7 + - - +
166A ILE* 3.9 9.4 - - + -
167A TYR 3.1 7.6 - - - +
168A MET* 3.9 7.2 - - + -
182A PHE* 3.8 3.2 - - - -
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Residues in contact with LYS 150 (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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149A ALA* 1.3 74.8 - - - +
151A VAL* 1.3 69.2 + - - +
152A LEU* 3.6 20.8 + - + +
166A ILE* 3.3 8.3 - - - +
167A TYR* 2.9 33.4 + - - +
182A PHE* 3.6 38.6 - - + -
1335A GOL 3.9 25.8 + - - +
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Residues in contact with VAL 151 (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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122A LYS* 4.1 32.3 - - + -
125A ALA* 4.2 15.0 - - + -
150A LYS* 1.3 78.7 + - - +
152A LEU* 1.3 70.1 + - - +
153A ASN 5.2 0.4 - - - +
164A GLU* 4.4 9.0 - - + -
165A ARG 3.1 17.7 - - - +
166A ILE* 3.8 24.7 - - + -
1335A GOL 3.5 17.1 + - - -
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Residues in contact with LEU 152 (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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150A LYS* 3.6 29.4 - - + +
151A VAL* 1.3 86.0 - - - +
153A ASN* 1.3 60.0 + - - +
154A ALA 3.9 0.7 + - - -
157A TYR* 3.7 29.4 - - + +
163A ASN 3.6 1.7 - - - +
164A GLU* 3.6 1.2 - - - -
165A ARG* 2.8 28.5 + - - +
167A TYR* 3.6 29.9 + - + -
182A PHE* 4.1 12.8 - - + -
183A PRO* 4.0 26.2 - - + -
310A VAL* 4.1 16.4 - - + -
314A ILE* 4.1 3.1 - - + -
1335A GOL 3.6 7.9 - - - +
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Residues in contact with ASN 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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151A VAL* 6.1 0.2 - - + -
152A LEU* 1.3 72.8 - - - +
154A ALA* 1.3 75.3 + - - +
155A LEU* 3.1 27.1 - - + +
156A ASP* 3.0 22.3 + - - +
157A TYR* 3.3 11.8 - - - -
161A GLN 3.3 17.6 + - - -
162A LYS* 3.3 9.2 + - - +
163A ASN 3.3 10.4 + - - -
164A GLU* 3.2 30.8 - - + +
1335A GOL 2.9 19.2 + - - +
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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