Contacts of the strand formed by residues 74 - 79 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B LYS* 3.7 11.7 + - - -
29B GLY 3.5 1.8 - - - +
31B LEU* 4.5 16.2 - - + +
70B VAL* 2.9 37.8 + - + +
71B LYS 4.1 0.3 - - - +
72B LYS 3.8 0.6 - - - -
73B CYS* 1.3 87.7 - - - +
75B GLY* 1.3 58.3 + - - +
76B GLY 3.5 23.6 - - - +
77B VAL* 4.1 8.1 - - + -
103B ILE* 3.6 35.5 - - + +
300B PHE* 4.2 18.4 - - + -
306B LEU* 4.7 3.1 - - + -
328B PHE* 4.7 4.3 - - + -
332B ALA* 4.0 20.0 - - + -
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG 4.3 1.9 - - - +
23B ILE* 3.6 28.1 - - - -
28B LYS* 3.8 20.3 - - - +
29B GLY 2.7 12.5 + - - -
74B ILE* 1.3 74.7 - - - +
76B GLY* 1.3 54.7 + - - -
102B GLY 4.9 0.5 - - - +
103B ILE* 3.6 3.6 - - - +
104B VAL* 2.9 31.7 + - - +
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 4.4 7.1 - - - +
29B GLY 3.4 3.8 + - - -
30B ILE* 3.3 9.5 - - - -
31B LEU 2.9 23.7 + - - -
74B ILE* 3.4 6.6 - - - +
75B GLY* 1.3 80.1 - - - +
77B VAL* 1.3 64.5 + - - -
103B ILE* 3.5 2.7 - - - -
104B VAL* 3.2 15.9 - - - -
145B PHE* 4.3 7.4 - - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 3.3 22.4 - - + +
33B ALA* 4.8 0.7 - - + -
64B PHE* 3.6 30.5 - - + -
74B ILE* 4.1 9.2 - - + -
76B GLY* 1.3 80.6 - - - +
78B ILE* 1.3 68.8 + - - +
79B PHE* 3.5 20.4 - - + -
98B ILE* 3.9 16.8 - - + -
103B ILE* 3.6 19.3 - - + -
104B VAL 2.9 7.7 + - - +
106B GLY 2.9 23.6 + - - -
145B PHE* 3.9 1.9 - - - -
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.6 26.9 - - + -
31B LEU 2.8 12.6 + - - +
32B ALA* 4.1 10.1 - - + -
33B ALA* 3.0 31.4 + - - +
34B ASP* 3.6 23.6 - - + +
77B VAL* 1.3 71.2 - - - +
79B PHE* 1.3 63.8 + - - +
106B GLY 3.5 4.9 - - - +
107B ILE 4.3 2.7 - - - -
108B LYS 4.1 11.4 - - - +
145B PHE* 3.6 14.8 - - + -
147B LYS* 4.0 28.3 - - + -
186B ILE* 4.1 13.2 - - + -
230B LYS* 4.1 3.6 - - - +
301B SER* 3.7 14.1 - - - +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 4.3 2.7 - - - -
34B ASP* 3.7 4.5 - - - +
64B PHE* 3.7 28.5 - + - -
77B VAL* 3.5 29.4 - - + -
78B ILE* 1.3 75.2 - - - +
80B PHE* 1.3 66.5 + - - +
83B THR* 3.5 22.0 - - + -
84B LEU* 3.7 24.7 - - + -
94B PHE* 3.8 19.5 - - + -
95B VAL* 4.2 12.6 - - + -
98B ILE* 4.1 18.6 - - + -
105B VAL* 3.6 24.5 - - + -
106B GLY 2.6 18.4 + - - +
107B ILE* 3.4 4.0 - - + -
108B LYS 3.2 24.6 + - - -
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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