Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 4MYF
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 PHE 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASP 3.0 18.4 + - - +
24A ILE* 3.2 10.5 - - + +
25A VAL 2.8 26.0 + - - +
100A VAL* 3.9 2.7 - - - -
105A ALA* 1.3 73.4 - - - +
107A PRO* 1.3 78.5 - - - +
108A PHE* 3.7 5.1 + - + -
266A VAL* 3.3 26.2 - - + -
267A MET* 3.4 21.8 - - - -
268A MET 3.3 19.3 - - - -
269A MET* 3.5 12.3 - - + -
294A PHE* 3.0 43.3 - + - -
298A PHE* 3.9 25.1 - + + -
301A ARG* 4.1 1.8 - - - -
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Residues in contact with PRO 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL 3.4 6.3 - - - +
27A ILE* 4.3 13.0 - - + -
97A VAL* 3.9 19.5 - - + +
100A VAL* 3.6 19.9 - - + -
101A LEU* 3.6 25.1 - - + -
105A ALA 3.5 7.2 - - - +
106A PHE* 1.3 87.5 - - - +
108A PHE* 1.3 58.3 + - - +
109A VAL* 4.2 1.6 - - + -
267A MET 3.4 18.8 - - - +
268A MET* 3.4 9.7 - - + +
269A MET 3.3 22.5 + - - +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.4 5.6 - - + -
25A VAL 2.8 11.7 + - - +
26A ILE* 3.3 12.3 - - + -
27A ILE* 2.9 25.0 + - - +
51A PHE* 3.7 29.2 - + - -
106A PHE* 3.7 10.0 + + + -
107A PRO* 1.3 73.7 - - - +
109A VAL* 1.3 62.5 + - - +
110A ILE* 3.9 18.6 - - + -
269A MET* 3.3 42.8 - - + -
271A MET* 4.0 38.1 - - + -
291A PHE* 3.7 38.8 - + + -
294A PHE* 5.6 1.1 - + - -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 3.2 20.6 - - + +
29A PHE* 4.3 6.1 - - + -
93A LEU* 4.0 16.4 - - + -
97A VAL* 3.8 18.6 - - + -
107A PRO 5.0 0.4 - - - -
108A PHE* 1.3 78.1 - - - +
110A ILE* 1.3 61.0 + - - +
116A GLN* 3.4 23.8 + - - +
120A ASN* 3.7 26.2 - - - +
268A MET* 4.0 10.3 - - + -
269A MET 3.1 6.5 + - - -
270A ASP* 3.3 11.2 - - + +
271A MET* 3.0 28.1 + - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.3 15.3 - - + -
27A ILE 2.9 19.9 + - - +
28A GLY* 3.5 10.4 - - - -
29A PHE 2.9 26.2 + - - -
47A GLY 4.4 0.2 - - - +
48A PRO* 3.5 16.8 - - + +
51A PHE* 3.7 45.1 - - + -
52A ARG* 5.1 3.4 - - + +
108A PHE* 3.9 12.0 + - + -
109A VAL* 1.3 73.2 - - - +
111A GLY* 1.3 72.2 + - - +
116A GLN* 4.0 1.8 - - - -
271A MET* 3.9 27.8 - - + +
274A LEU* 4.7 9.4 - - + -
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE 3.6 2.9 - - - -
47A GLY* 3.6 6.2 - - - -
48A PRO* 3.3 21.0 - - - +
110A ILE* 1.3 85.5 - - - +
112A GLY* 1.3 69.2 + - - -
116A GLN* 3.4 15.9 + - - -
271A MET 2.9 16.4 + - - -
273A GLU 5.0 1.3 - - - -
274A LEU* 4.4 6.0 - - - +
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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