Contacts of the strand formed by residues 297 - 302 (chain I) in PDB entry 1XFB
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 ALA 297 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24I VAL* 3.7 37.9 - - + +
266I PRO 3.0 18.0 + - - +
267I GLY* 3.8 1.6 - - - -
268I VAL* 2.8 24.4 + - - +
296I TRP* 1.3 74.4 - - - +
298I LEU* 1.3 63.7 + - - +
299I THR* 3.8 7.6 - - + -
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Residues in contact with LEU 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I VAL* 4.3 5.6 - - + -
257I LEU* 3.9 13.9 - - + -
268I VAL* 3.6 17.9 - - + -
270I PHE* 4.0 10.3 - - + -
284I LEU* 3.3 4.8 - - - +
287I ILE* 3.4 25.1 - - + -
288I ASN* 2.8 35.2 + - - +
294I ARG* 3.5 40.6 - - + +
296I TRP* 3.4 32.9 + - + +
297I ALA* 1.3 77.4 - - - +
299I THR* 1.3 63.5 + - - +
339I ALA 4.2 1.1 + - - +
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Residues in contact with THR 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I VAL* 4.3 20.8 - - + +
25I ALA 5.0 0.2 - - - +
26I PRO* 6.2 0.2 - - + -
27I GLY 5.5 0.9 - - - +
28I LYS 3.0 30.8 + - - +
29I GLY* 3.5 2.1 - - - -
268I VAL 3.2 9.6 + - - -
269I THR* 4.2 8.9 - - - +
270I PHE* 3.1 31.0 + - - +
284I LEU* 3.8 8.8 - - - +
297I ALA* 3.8 6.0 - - + -
298I LEU* 1.3 81.5 - - - +
300I PHE* 1.3 83.6 + - - -
339I ALA* 3.8 22.0 - - + +
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Residues in contact with PHE 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I LYS 4.1 2.0 - - - -
29I GLY* 3.2 25.3 - - - -
30I ILE* 2.8 52.8 + - - +
73I CYS 3.5 14.6 - - - -
74I ILE* 4.2 7.2 - - + -
269I THR* 3.9 5.7 - - - -
270I PHE 3.6 4.7 - - - -
284I LEU* 3.7 9.9 - - + -
299I THR* 1.3 93.8 + - - +
301I SER* 1.3 57.1 + - - +
302I TYR* 3.3 38.1 - + + -
306I LEU* 3.8 17.7 - - + -
332I ALA 4.4 5.2 - - - -
335I ASN* 3.5 42.0 - - + -
336I GLY* 3.9 3.6 - - - -
339I ALA* 4.4 1.3 - - + -
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Residues in contact with SER 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ILE* 3.4 27.8 - - - +
32I ALA* 4.5 1.5 - - - +
78I ILE* 3.7 5.5 - - - +
186I ILE* 4.9 0.2 - - - +
230I LYS* 3.3 38.3 + - - +
269I THR* 3.2 33.3 + - - -
270I PHE 2.7 13.7 + - - +
271I LEU* 3.8 4.9 - - - -
272I SER 4.3 0.3 + - - -
300I PHE* 1.3 71.2 - - - +
302I TYR* 1.3 61.0 + - - +
303I GLY 4.1 0.5 + - - -
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Residues in contact with TYR 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ILE 3.3 8.7 + - - +
31I LEU* 4.2 0.7 - - - +
32I ALA* 2.9 27.0 + - - -
233I MET* 3.2 16.3 - - + +
270I PHE* 3.5 22.2 - - + -
271I LEU 4.1 0.7 - - - -
272I SER* 3.5 22.2 - - - -
280I ALA* 3.1 40.4 + - + -
284I LEU* 3.5 9.4 - - + +
300I PHE* 3.3 29.4 - + + -
301I SER* 1.3 75.6 - - - +
303I GLY* 1.3 62.0 + - - +
305I ALA* 3.4 19.7 - - + -
306I LEU* 3.7 22.8 - - + +
335I ASN* 3.5 30.7 - - - -
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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