Contacts of the strand formed by residues 206 - 211 (chain A) in PDB entry 4LP4
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 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 4.6 0.2 - - - +
133A LEU* 4.2 8.1 - - + -
141A VAL* 4.0 12.8 - - + -
157A TRP* 4.7 5.6 - - + -
158A HIS 3.2 6.5 - - - +
159A LEU* 3.6 25.8 - - + -
164A LEU* 4.2 11.2 - - + -
192A LEU* 3.9 17.5 - - + -
194A VAL* 4.0 38.1 - - + -
196A PRO* 6.3 0.2 - - + -
204A PRO* 3.6 28.5 - - + -
205A THR* 1.3 75.9 - - - +
207A SER* 1.3 61.7 + - - +
224A PRO* 3.3 5.1 - - - +
225A ILE* 2.8 50.0 + - + +
227A PRO* 4.0 24.7 - - + -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.4 2.9 - - - -
157A TRP* 3.3 10.3 - - - -
158A HIS* 2.7 42.8 + - - +
205A THR* 5.9 1.1 - - - -
206A PHE* 1.3 76.9 - - - +
208A CYS* 1.3 60.6 + - - +
221A ARG* 3.3 36.4 + - - -
222A THR* 3.9 18.6 - - - -
224A PRO* 4.4 9.0 - - - -
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Residues in contact with CYS 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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126A ILE* 4.3 1.9 - - + +
144A CYS* 2.0 54.1 - - + -
155A LEU* 4.0 18.8 - - - -
156A SER 3.4 12.8 - - - +
157A TRP* 4.2 13.5 - - + -
158A HIS* 4.7 1.3 - - - -
207A SER* 1.3 74.4 - - - +
209A SER* 1.3 66.1 + - - +
221A ARG* 3.6 3.2 - - - +
222A THR* 2.8 41.2 + - + +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 4.9 1.6 - - - -
154A THR 3.8 0.5 - - - +
155A LEU* 3.5 5.5 - - - +
156A SER* 3.0 35.0 + - - -
158A HIS* 3.0 25.4 + - - -
208A CYS* 1.3 80.9 - - - +
210A PHE* 1.3 62.0 + - - +
211A SER* 4.0 4.7 + - - -
219A ALA* 4.8 8.5 - - - +
220A LEU 3.1 13.2 - - - -
221A ARG* 4.2 15.3 - - - -
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN 5.7 0.2 - - - -
121A PRO* 3.6 24.2 - - + -
124A PRO* 4.5 8.6 - - + +
146A SER* 3.5 22.0 - - - +
149A SER* 3.6 24.9 - - - -
151A PRO 4.7 1.3 - - - -
152A ALA 3.2 22.0 - - - -
153A GLY* 4.0 5.2 - - - -
154A THR 3.5 10.8 - - - -
155A LEU* 4.1 11.2 - - + -
188A LEU* 3.9 8.5 - - + -
209A SER* 1.3 72.3 - - - +
211A SER* 1.3 59.7 + - - +
212A PRO* 3.5 35.0 - - + -
219A ALA* 3.2 9.6 - - - +
220A LEU* 2.8 50.4 + - + +
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLY* 3.3 1.6 - - - -
154A THR* 2.9 47.2 + - - -
156A SER* 4.8 9.5 + - - -
209A SER* 4.0 3.3 + - - -
210A PHE* 1.3 75.1 + - - +
212A PRO* 1.3 70.7 - - - +
213A GLY* 3.1 6.6 + - - -
219A ALA* 4.7 9.1 - - - +
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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