Contacts of the strand formed by residues 207 - 213 (chain A) in PDB entry 4X5O
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A CYS* 3.7 30.5 - - + -
199A LEU* 3.5 30.1 - - + -
200A SER* 3.0 45.3 - - - -
204A ILE* 6.2 0.7 - - + -
205A GLY 4.0 13.7 - - - -
206A ASP* 1.3 90.7 + - - +
208A LEU* 1.3 66.9 + - - +
209A VAL* 4.6 6.5 - - + -
317A LYS* 3.6 45.4 - - + +
339A VAL 3.3 13.7 - - - +
340A LEU* 4.2 11.0 - - + -
341A LEU* 4.5 5.0 - - - +
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Residues in contact with LEU 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 PHE* 1.3 77.6 - - - +
209A VAL* 1.3 74.6 + - - +
210A LYS* 4.0 19.7 + - + +
316A ASP 4.8 4.0 - - - +
317A LYS* 4.0 6.1 - - - +
318A ILE* 3.7 10.5 - - - +
319A SER* 3.6 39.0 - - - +
337A GLU 3.9 0.2 - - - +
338A ALA* 3.3 4.2 - - - +
339A VAL* 2.9 36.9 + - + +
341A LEU* 4.6 19.3 - - + +
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Residues in contact with VAL 209 (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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192A LEU* 4.2 20.9 - - + -
195A MET* 3.7 33.7 - - + -
196A CYS* 3.9 20.2 - - - -
207A PHE* 4.6 6.3 - - + -
208A LEU* 1.3 79.3 - - - +
210A LYS* 1.3 70.5 + - - +
211A VAL* 4.6 5.2 - - + -
317A LYS 3.2 20.3 + - - +
318A ILE* 3.4 8.5 - - + +
319A SER 2.8 27.3 + - - -
336A TYR* 4.8 0.2 - - + -
337A GLU 3.5 11.2 - - - +
338A ALA* 4.5 2.5 - - + -
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Residues in contact with LYS 210 (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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208A LEU* 4.6 20.4 - - + -
209A VAL* 1.3 74.6 - - - +
211A VAL* 1.3 60.5 + - - +
242A ASP* 3.2 39.6 + - + +
319A SER* 3.4 6.7 - - - +
321A ASP* 3.5 30.5 + - + +
324A LEU* 3.5 21.5 - - + +
336A TYR* 3.6 3.5 - - - -
337A GLU* 2.7 44.6 + - + +
339A VAL* 4.0 26.8 - - + +
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Residues in contact with VAL 211 (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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192A LEU* 4.2 6.3 - - + -
209A VAL* 4.6 3.8 - - + -
210A LYS* 1.3 76.9 - - - +
212A ASN* 1.3 65.8 + - - +
302A LEU* 3.7 29.4 - - + -
305A LEU* 4.8 2.2 - - + -
306A PHE* 4.9 2.2 - - + -
318A ILE* 3.6 33.9 - - + -
319A SER 3.0 9.7 + - - +
320A PHE* 3.0 17.7 - - + -
321A ASP 2.9 23.9 + - - -
324A LEU* 4.2 1.8 - - - +
334A VAL* 5.4 0.2 - - + -
335A ILE 3.5 2.0 - - - -
336A TYR* 3.4 33.7 - - + -
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Residues in contact with ASN 212 (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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211A VAL* 1.3 78.6 - - - +
213A ASP* 1.3 77.2 + - - +
216A ILE* 4.1 9.1 - - - +
217A LEU* 4.0 18.6 - - - +
220A MET* 6.2 0.4 - - - +
302A LEU* 4.6 4.0 - - - -
320A PHE* 3.3 21.9 - - - -
321A ASP 3.5 12.7 + - - +
322A LEU* 3.6 19.0 + - - +
324A LEU* 2.8 34.6 + - + +
334A VAL* 3.3 3.9 - - - +
335A ILE* 2.5 44.6 + - + +
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Residues in contact with ASP 213 (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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185A MET* 5.7 0.2 - - - +
212A ASN* 1.3 93.0 + - - +
214A ARG* 1.3 64.4 + - - +
215A ARG* 2.7 54.2 + - - +
216A ILE* 3.4 30.3 + - + +
217A LEU* 3.4 10.4 + - - +
298A GLY* 3.7 18.2 - - - +
301A ASP* 4.6 4.2 - - - +
302A LEU* 4.4 5.3 - - + +
333A GLY* 3.3 21.8 - - - +
334A VAL* 3.5 8.9 + - - +
335A ILE* 4.7 2.5 - - - -
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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