Contacts of the strand formed by residues 74 - 79 (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 ILE 74 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28K LYS* 3.7 12.5 + - - -
29K GLY 3.5 2.5 - - - +
31K LEU* 4.5 16.6 - - + +
70K VAL* 2.9 37.7 + - + +
71K LYS 4.1 0.3 - - - +
72K LYS 3.8 1.2 - - - -
73K CYS* 1.3 87.6 - - - +
75K GLY* 1.3 59.1 + - - +
76K GLY 3.5 23.3 - - - +
77K VAL* 4.1 8.5 - - + -
103K ILE* 3.6 35.1 - - + +
300K PHE* 4.2 17.9 - - + -
306K LEU* 4.7 2.9 - - + -
328K PHE* 4.7 4.7 - - + -
332K ALA* 4.0 20.6 - - + -
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Residues in contact with GLY 75 (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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22K ARG 4.3 2.1 - - - +
23K ILE* 3.6 28.3 - - - -
28K LYS* 3.8 21.7 - - - +
29K GLY 2.7 11.7 + - - -
74K ILE* 1.3 74.3 - - - +
76K GLY* 1.3 54.6 + - - -
102K GLY 4.9 0.2 - - - +
103K ILE* 3.6 4.1 - - - +
104K VAL* 2.9 31.5 + - - +
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Residues in contact with GLY 76 (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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23K ILE* 4.4 7.8 - - - +
29K GLY 3.4 4.2 + - - -
30K ILE* 3.3 8.5 - - - -
31K LEU 2.9 24.6 + - - -
74K ILE* 3.4 6.2 - - - +
75K GLY* 1.3 81.8 - - - +
77K VAL* 1.3 64.1 + - - -
103K ILE* 3.5 2.7 - - - +
104K VAL* 3.2 15.5 - - - -
145K PHE* 4.3 7.4 - - - -
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Residues in contact with VAL 77 (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* 3.3 23.6 - - + +
33K ALA* 4.8 0.4 - - + -
64K PHE* 3.6 31.9 - - + -
74K ILE* 4.1 8.5 - - + -
76K GLY* 1.3 79.8 - - - +
78K ILE* 1.3 67.7 + - - +
79K PHE* 3.5 19.8 - - + -
98K ILE* 3.9 16.2 - - + -
103K ILE* 3.6 20.2 - - + -
104K VAL 2.9 8.2 + - - +
105K VAL 3.8 0.2 - - - -
106K GLY 2.9 23.7 + - - -
145K PHE* 3.9 2.1 - - - -
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Residues in contact with ILE 78 (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 26.5 - - + -
31K LEU 2.8 12.0 + - - +
32K ALA* 4.1 9.9 - - + -
33K ALA* 3.0 30.5 + - - +
34K ASP* 3.6 22.7 - - + +
77K VAL* 1.3 71.4 - - - +
79K PHE* 1.3 65.5 + - - +
106K GLY 3.5 4.3 - - - +
107K ILE 4.3 3.4 - - - +
108K LYS 4.1 11.4 - - - +
145K PHE* 3.6 15.9 - - + -
147K LYS* 4.0 27.6 - - + -
186K ILE* 4.1 13.9 - - + -
230K LYS* 4.1 3.6 - - - +
301K SER* 3.7 13.7 - - - +
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Residues in contact with PHE 79 (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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33K ALA* 4.3 3.1 - - - -
34K ASP* 3.7 4.2 - - - +
64K PHE* 3.7 29.4 - + - -
77K VAL* 3.5 28.7 - - + -
78K ILE* 1.3 75.9 - - - +
80K PHE* 1.3 65.3 + - - +
83K THR* 3.5 21.5 - - + -
84K LEU* 3.7 25.6 - - + -
94K PHE* 3.8 19.7 - - + -
95K VAL* 4.2 12.8 - - + -
98K ILE* 4.1 18.6 - - + -
105K VAL* 3.6 24.2 - - + -
106K GLY 2.6 18.4 + - - +
107K ILE* 3.4 3.7 - - + -
108K LYS 3.2 24.9 + - - -
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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