Contacts of the strand formed by residues 202 - 206 (chain A) in PDB entry 1U54
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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.2 38.2 + - - +
126A LEU* 4.1 13.0 - - + -
128A LEU* 3.8 42.0 - - + -
157A VAL* 4.1 12.6 - - + -
158A LYS 3.9 4.0 - - - -
159A CYS* 4.1 12.8 - - + +
174A PHE* 3.6 7.4 - - - -
195A VAL* 3.3 5.9 - - - -
196A VAL* 2.8 59.7 + - + +
198A THR 4.5 1.0 + - - -
200A PRO* 3.3 24.2 + - - +
201A MET* 1.3 79.9 - - - +
203A MET* 1.3 59.8 + - - +
204A VAL* 4.1 0.4 - - + -
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Residues in contact with MET 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.3 5.2 - - - -
158A LYS* 2.9 59.1 + - + +
174A PHE* 3.8 25.7 - - + +
177A GLU* 3.3 52.7 - - + +
178A VAL* 4.0 19.5 - - + +
181A MET* 3.9 16.2 - - - +
192A LEU* 4.1 13.9 - - + -
194A GLY 4.0 2.0 - - - -
195A VAL* 4.8 0.4 - - + +
202A LYS* 1.3 71.6 - - - +
204A VAL* 1.3 62.7 + - - +
205A THR* 3.5 10.3 + - + +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 4.0 21.8 - - + -
126A LEU* 4.3 22.0 - - + -
145A TRP* 4.6 5.6 - - + -
155A VAL* 3.6 39.9 - - + -
156A ALA 3.6 2.7 - - - +
157A VAL* 4.8 3.1 - - + -
192A LEU* 3.6 1.6 - - - +
193A TYR* 2.8 33.2 + - + +
194A GLY 2.9 22.9 + - - +
196A VAL* 4.4 10.8 - - + -
202A LYS 4.6 2.0 - - - +
203A MET* 1.3 75.8 - - - +
205A THR* 1.3 58.6 + - - +
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Residues in contact with THR 205 (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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101A ACP 3.7 5.4 + - - -
155A VAL* 3.3 9.4 - - - +
156A ALA* 2.9 51.1 + - - +
157A VAL* 5.2 0.2 - - - -
158A LYS* 5.2 7.3 + - + +
181A MET* 4.2 22.4 - - - -
190A ILE* 3.7 13.9 - - + -
191A ARG 3.3 13.9 - - - +
192A LEU* 4.4 2.7 - - - -
193A TYR* 3.9 4.3 - - - -
203A MET* 3.5 18.5 + - + +
204A VAL* 1.3 77.7 - - - +
206A GLU* 1.3 58.6 + - - +
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Residues in contact with GLU 206 (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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101A ACP 3.0 21.7 + - - -
156A ALA 4.3 0.2 - - - -
186A HIS 5.2 0.3 - - - +
189A LEU 4.1 2.6 - - - +
190A ILE* 3.5 12.0 - - + +
191A ARG* 3.0 51.2 + - + +
193A TYR* 3.6 31.5 + - + +
205A THR* 1.3 72.9 - - - +
207A LEU* 1.3 69.2 + - - +
267A LYS* 2.3 49.3 + - - +
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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