Contacts of the strand formed by residues 29 - 33 (chain K) 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 GLY 29 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23K ILE 4.8 2.2 - - - -
28K LYS* 1.3 74.1 - - - +
30K ILE* 1.3 64.3 + - - -
73K CYS 2.7 10.3 + - - -
74K ILE* 3.5 4.6 - - - -
75K GLY* 2.7 24.5 + - - -
76K GLY 3.4 3.1 + - - -
299K THR* 3.5 10.1 - - - -
300K PHE* 3.2 25.3 - - - -
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Residues in contact with ILE 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K ILE* 3.6 32.8 - - + -
24K VAL* 6.0 0.7 - - + -
29K GLY* 1.3 77.0 - - - +
31K LEU* 1.3 65.2 + - - +
74K ILE* 4.9 0.2 - - - -
76K GLY 3.3 13.2 - - - +
78K ILE* 3.6 33.9 - - + -
145K PHE* 4.4 3.6 - - + -
186K ILE* 3.8 25.8 - - + -
228K LEU* 4.5 0.7 - - + -
269K THR* 3.9 22.9 - - + -
300K PHE* 2.8 24.4 + - - +
301K SER* 3.4 9.4 - - - +
302K TYR 3.3 24.3 + - - +
306K LEU* 3.7 1.0 - - - +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 1.3 71.8 - - - +
32K ALA* 1.3 62.1 + - - +
33K ALA* 3.4 6.1 + - + +
63K LEU* 4.2 19.5 - - + -
64K PHE* 4.3 11.0 - - + -
74K ILE* 4.5 12.4 - - + +
76K GLY 2.9 11.6 + - - +
77K VAL* 3.3 26.0 - - + -
78K ILE 2.8 26.7 + - - -
302K TYR 4.2 0.4 - - - +
306K LEU* 3.7 26.2 - - + -
307K GLN* 3.8 22.9 - - + +
328K PHE* 3.7 28.3 - - + -
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Residues in contact with ALA 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE 3.6 0.8 + - - -
31K LEU* 1.3 71.4 - - - +
33K ALA* 1.3 56.9 + - - +
34K ASP* 3.4 20.5 + - - +
35K GLU* 3.7 4.7 - - - +
78K ILE* 4.1 12.3 - - + -
147K LYS* 5.1 0.7 - - - +
230K LYS* 4.1 20.6 - - - +
301K SER* 4.4 3.1 - - - +
302K TYR 2.9 26.8 + - - +
303K GLY* 3.5 11.0 - - - +
307K GLN* 3.3 16.6 + - - -
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Residues in contact with ALA 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LEU* 3.4 16.0 + - + -
32K ALA* 1.3 72.7 - - - +
34K ASP* 1.3 56.5 + - - +
35K GLU* 3.0 16.2 + - - +
60K ARG* 3.1 24.6 + - - +
63K LEU* 4.4 14.1 - - + -
64K PHE* 4.4 22.4 - - + -
77K VAL* 4.8 0.4 - - + -
78K ILE 3.0 15.8 + - - +
79K PHE* 4.3 0.7 - - - -
80K PHE 3.7 8.3 + - - -
83K THR* 4.9 1.4 + - - +
307K GLN* 4.2 1.3 - - - +
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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