Contacts of the strand formed by residues 297 - 302 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24L VAL* 3.7 37.7 - - + +
266L PRO 3.0 18.5 + - - +
267L GLY* 3.8 1.6 - - - -
268L VAL 2.8 25.0 + - - -
296L TRP* 1.3 75.0 - - - +
298L LEU* 1.3 63.2 + - - +
299L THR* 3.8 7.2 - - + -
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Residues in contact with LEU 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254L VAL* 4.3 5.6 - - + -
257L LEU* 3.9 13.7 - - + -
268L VAL* 3.6 17.7 - - + -
270L PHE* 4.0 11.4 - - + -
284L LEU* 3.3 4.9 - - - +
287L ILE* 3.4 25.1 - - + +
288L ASN* 2.8 35.8 + - - +
294L ARG* 3.5 40.8 - - + +
296L TRP* 3.4 33.1 + - + +
297L ALA* 1.3 77.2 - - - +
299L THR* 1.3 62.3 + - - +
339L ALA 4.2 1.3 + - - +
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Residues in contact with THR 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L VAL* 4.3 20.3 - - + +
25L ALA 5.0 0.2 - - - +
26L PRO* 6.2 0.2 - - + -
27L GLY 5.5 1.8 - - - +
28L LYS 3.0 30.1 + - - +
29L GLY* 3.5 2.1 - - - -
268L VAL 3.2 10.0 + - - -
269L THR* 4.2 9.1 - - - +
270L PHE* 3.1 31.5 + - - +
284L LEU* 3.8 8.2 - - - +
297L ALA* 3.8 5.8 - - + -
298L LEU* 1.3 81.4 - - - +
300L PHE* 1.3 83.6 + - - +
339L ALA* 3.8 22.9 - - + +
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Residues in contact with PHE 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L LYS 4.1 2.0 - - - -
29L GLY* 3.2 24.5 - - - -
30L ILE* 2.8 53.5 + - - +
73L CYS 3.5 13.7 - - - -
74L ILE* 4.2 7.2 - - + -
269L THR* 3.9 5.5 - - - -
270L PHE 3.6 4.7 - - - -
284L LEU* 3.7 9.0 - - + -
299L THR* 1.3 94.6 + - - +
301L SER* 1.3 57.7 + - - +
302L TYR* 3.3 40.4 - + + -
306L LEU* 3.8 17.3 - - + -
332L ALA 4.4 5.2 - - - -
335L ASN* 3.5 42.4 - - + -
336L GLY* 3.9 3.6 - - - -
339L ALA* 4.4 1.3 - - + -
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Residues in contact with SER 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ILE* 3.4 28.4 - - - +
32L ALA* 4.5 1.7 - - - +
78L ILE* 3.7 5.9 - - - +
186L ILE* 4.9 0.3 - - - +
230L LYS* 3.3 37.7 + - - +
269L THR* 3.2 33.6 + - - -
270L PHE 2.7 12.9 + - - +
271L LEU* 3.8 4.7 - - - -
272L SER 4.3 0.2 + - - -
300L PHE* 1.3 71.2 - - - +
302L TYR* 1.3 61.3 + - - +
303L GLY 4.1 0.5 + - - -
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Residues in contact with TYR 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ILE 3.3 7.1 + - - +
31L LEU* 4.2 0.7 - - - +
32L ALA* 2.9 26.8 + - - -
233L MET* 3.2 16.1 - - + +
270L PHE* 3.5 22.7 - - + -
271L LEU 4.1 1.1 - - - -
272L SER* 3.5 21.3 - - - -
280L ALA* 3.1 41.8 + - + -
284L LEU* 3.5 9.2 - - + +
300L PHE* 3.3 28.4 - + + -
301L SER* 1.3 75.8 - - - +
303L GLY* 1.3 61.5 + - - +
305L ALA* 3.4 20.0 - - + -
306L LEU* 3.7 23.0 - - + +
335L ASN* 3.5 31.2 - - - -
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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
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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