Contacts of the strand formed by residues 204 - 208 (chain A) in PDB entry 1IEW
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 CYS 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.9 9.4 - - + -
143A ALA 3.4 12.1 + - - +
144A PHE* 3.6 10.6 - - - -
145A ALA* 2.6 35.7 + - - -
146A PRO 3.1 4.6 - - - +
203A ALA* 1.3 73.1 - - - +
205A ALA* 1.3 64.1 + - - +
206A LYS* 3.4 4.0 + - - +
246A VAL* 4.3 1.1 - - - -
248A THR* 3.2 20.9 - - - +
249A VAL 4.1 0.2 - - - -
250A MET* 3.5 53.8 - - - -
283A ILE* 4.4 0.2 - - - -
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Residues in contact with ALA 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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146A PRO* 3.5 9.0 - - + -
148A ILE* 4.2 7.2 - - + -
177A ILE* 5.1 2.9 - - + -
204A CYS* 1.3 70.2 - - - +
206A LYS* 1.3 58.6 + - - +
238A TYR* 3.8 24.6 - - + -
241A ALA* 4.2 13.9 - - + -
246A VAL* 3.7 18.1 - - + +
248A THR 3.2 9.4 + - - +
249A VAL* 3.4 14.2 - - + +
250A MET 3.2 19.4 + - - -
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Residues in contact with LYS 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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95A ASP* 3.2 7.9 + - - -
97A VAL* 3.8 12.3 - - - +
144A PHE 2.7 31.8 + - - +
146A PRO 3.2 5.0 + - - +
147A CYS* 3.1 27.8 - - - +
148A ILE* 2.7 33.4 + - - +
149A ALA 3.8 2.9 + - - -
158A ARG* 4.6 4.2 - - - +
161A GLU* 4.8 0.9 + - - -
204A CYS* 4.1 3.6 - - - +
205A ALA* 1.3 75.8 - - - +
207A HIS* 1.3 93.4 + - + +
238A TYR* 3.2 9.2 + - - -
250A MET* 3.8 20.4 - - + -
430A TRP* 5.5 1.0 - - - -
620A G2F 2.8 30.6 + - - +
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Residues in contact with HIS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A CYS* 4.2 10.7 - - - -
156A TRP* 5.3 1.8 - + - -
158A ARG* 3.2 31.9 + - - -
206A LYS* 1.3 101.1 + - + +
208A PHE* 1.3 64.5 + - - +
209A VAL* 3.2 6.1 + - - -
211A ASP* 2.9 51.0 + - + +
238A TYR* 2.9 4.8 + - - -
250A MET* 3.5 7.9 - - + +
251A ILE 4.8 0.2 - - - -
252A SER* 3.4 26.9 - - - +
285A ASP* 3.5 21.5 - - - -
620A G2F 2.6 24.0 + - - -
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Residues in contact with PHE 208 (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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207A HIS* 1.3 67.5 - - - +
209A VAL* 1.3 59.5 + - + +
235A MET* 3.7 38.4 - - + -
238A TYR* 2.8 29.1 + + + +
249A VAL* 3.7 16.2 - - + -
250A MET 2.9 17.3 + - - +
251A ILE* 3.5 19.7 - - + +
252A SER* 3.0 20.9 + - - -
261A MET* 3.2 31.4 - - + +
267A LEU* 3.6 31.2 - - + -
268A VAL* 3.9 2.5 - - + -
271A TYR* 4.6 0.9 - + - -
272A LEU* 3.7 35.4 - - + -
276A LEU* 5.0 0.2 - - + -
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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
------------------------------------------------------------
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