Contacts of the strand formed by residues 74 - 79 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28H LYS* 3.7 11.7 + - - -
29H GLY 3.5 2.5 - - - +
31H LEU* 4.5 16.6 - - + +
70H VAL* 2.9 39.3 + - + +
71H LYS 4.1 0.2 - - - +
72H LYS 3.8 0.8 - - - -
73H CYS* 1.3 87.1 - - - +
75H GLY* 1.3 60.1 + - - +
76H GLY 3.5 23.1 - - - +
77H VAL* 4.1 8.3 - - + -
103H ILE* 3.6 35.3 - - + +
300H PHE* 4.2 18.2 - - + -
306H LEU* 4.7 3.1 - - + -
328H PHE* 4.7 4.5 - - + -
332H ALA* 4.0 19.5 - - + -
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Residues in contact with GLY 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ARG 4.3 1.9 - - - +
23H ILE* 3.6 27.6 - - - -
28H LYS* 3.8 20.9 - - - +
29H GLY 2.7 12.7 + - - -
74H ILE* 1.3 73.6 - - - +
76H GLY* 1.3 55.1 + - - -
102H GLY 4.9 0.3 - - - +
103H ILE* 3.6 3.9 - - - +
104H VAL* 2.9 30.8 + - - +
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Residues in contact with GLY 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ILE* 4.4 7.4 - - - +
29H GLY 3.4 4.0 + - - -
30H ILE* 3.3 8.6 - - - -
31H LEU 2.9 24.3 + - - -
74H ILE* 3.4 6.3 - - - +
75H GLY* 1.3 80.9 - - - +
77H VAL* 1.3 63.8 + - - -
103H ILE* 3.5 3.6 - - - +
104H VAL* 3.2 15.7 - - - -
145H PHE* 4.3 7.6 - - - -
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Residues in contact with VAL 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 3.3 23.1 - - + +
33H ALA* 4.8 0.9 - - + -
64H PHE* 3.6 30.7 - - + -
74H ILE* 4.1 8.7 - - + -
76H GLY* 1.3 80.8 - - - +
78H ILE* 1.3 66.5 + - - +
79H PHE* 3.5 21.3 - - + -
98H ILE* 3.9 15.9 - - + -
103H ILE* 3.6 20.9 - - + -
104H VAL 2.9 8.3 + - - +
105H VAL* 3.8 0.2 - - - -
106H GLY 2.9 23.6 + - - -
145H PHE* 3.9 2.6 - - - -
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Residues in contact with ILE 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ILE* 3.6 26.2 - - + -
31H LEU 2.8 11.2 + - - +
32H ALA* 4.1 10.1 - - + -
33H ALA* 3.0 30.7 + - - +
34H ASP* 3.6 22.7 - - + +
77H VAL* 1.3 72.1 - - - +
79H PHE* 1.3 64.3 + - - +
106H GLY 3.5 4.7 - - - +
107H ILE 4.3 3.6 - - - -
108H LYS 4.1 11.0 - - - +
145H PHE* 3.6 14.6 - - + -
147H LYS* 4.0 28.0 - - + +
186H ILE* 4.1 13.7 - - + -
230H LYS* 4.1 3.4 - - - +
301H SER* 3.7 14.4 - - - +
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Residues in contact with PHE 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ALA* 4.3 2.9 - - - -
34H ASP* 3.7 5.2 - - - +
64H PHE* 3.7 29.4 - + - -
77H VAL* 3.5 28.9 - - + -
78H ILE* 1.3 75.5 - - - +
80H PHE* 1.3 64.0 + - - +
83H THR* 3.5 22.0 - - + -
84H LEU* 3.7 25.4 - - + -
94H PHE* 3.8 19.1 - - + -
95H VAL* 4.2 12.3 - - + -
98H ILE* 4.1 18.2 - - + -
105H VAL* 3.6 25.1 - - + -
106H GLY 2.6 19.1 + - - +
107H ILE* 3.4 3.5 - - + -
108H 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