Contacts of the strand formed by residues 106 - 111 (chain B) in PDB entry 4MXR
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASP 3.0 17.8 + - - +
24B ILE* 3.2 10.1 - - + +
25B VAL 2.7 31.6 + - - -
100B VAL* 4.0 2.0 - - - -
105B ALA* 1.3 72.2 - - - +
107B PRO* 1.3 72.0 - - - +
108B PHE* 4.3 4.5 - - + -
266B VAL* 3.3 27.6 - - + -
267B MET* 3.2 22.0 - - + -
268B MET 3.3 19.3 - - - -
269B MET* 3.5 11.7 - - + -
294B PHE* 3.0 48.0 - + - -
298B PHE* 4.0 22.0 - + + -
301B ARG* 4.1 1.6 - - - -
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Residues in contact with PRO 107 (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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25B VAL 3.4 6.7 - - - +
27B ILE* 4.3 14.4 - - + -
97B VAL* 4.1 16.2 - - + +
100B VAL* 3.7 23.8 - - + -
101B LEU* 3.7 23.6 - - + -
105B ALA 3.5 5.8 - - - +
106B PHE* 1.3 88.2 - - - +
108B PHE* 1.3 59.9 + - - +
109B VAL* 4.9 0.9 - - + -
267B MET 3.3 18.4 - - - +
268B MET* 3.5 10.7 - - + +
269B MET 3.3 21.5 + - - +
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Residues in contact with PHE 108 (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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24B ILE* 4.4 7.6 - - + -
25B VAL 2.8 12.2 + - - +
26B ILE* 3.3 12.0 - - + -
27B ILE 2.9 24.3 + - - +
51B PHE* 3.7 28.0 - + - -
106B PHE* 3.8 7.1 + + + -
107B PRO* 1.3 72.1 - - - +
109B VAL* 1.3 62.5 + - - +
110B ILE* 3.9 17.7 - - + -
269B MET* 3.3 50.3 - - + -
271B MET* 3.9 33.0 - - + -
291B PHE* 3.6 39.7 - + + -
294B PHE* 5.6 0.9 - + - -
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Residues in contact with VAL 109 (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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27B ILE* 3.3 18.6 - - + +
29B PHE* 4.2 6.5 - - + -
93B LEU* 3.9 20.2 - - + -
97B VAL* 3.8 28.7 - - + -
107B PRO 4.9 0.7 - - - -
108B PHE* 1.3 81.6 - - - +
110B ILE* 1.3 60.9 + - - +
111B GLY 3.8 0.2 + - - -
116B GLN* 3.1 24.1 + - - +
120B ASN* 3.9 17.0 - - - +
268B MET* 4.0 9.4 - - + -
269B MET 3.0 8.1 + - - -
270B ASP* 3.3 4.8 - - + +
271B MET* 2.9 27.2 + - - +
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Residues in contact with ILE 110 (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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26B ILE* 4.4 14.6 - - + -
27B ILE 3.0 14.9 + - - +
28B GLY* 4.0 8.5 - - - -
29B PHE 3.0 24.1 + - - -
47B GLY 4.6 0.2 - - - +
48B PRO* 3.5 19.0 - - + +
51B PHE* 3.7 44.2 - - + -
52B ARG* 5.4 3.1 - - - +
108B PHE* 3.9 12.0 + - + -
109B VAL* 1.3 71.5 - - - +
111B GLY* 1.3 75.0 + - - +
116B GLN* 4.0 1.8 - - - -
271B MET* 3.7 28.9 - - + +
274B LEU* 4.6 10.3 - - + -
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Residues in contact with GLY 111 (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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29B PHE 3.6 3.1 - - - -
47B GLY* 3.7 6.6 - - - -
48B PRO* 3.4 16.7 - - - +
110B ILE* 1.3 88.5 - - - +
112B GLY* 1.3 69.8 + - - -
116B GLN* 3.5 15.5 - - - +
271B MET 2.9 16.5 + - - +
273B GLU 4.8 2.0 - - - -
274B LEU* 4.4 5.4 - - - +
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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