Contacts of the strand formed by residues 101 - 105 (chain Z) in PDB entry 4MXW
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 GLY 101 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96Z PRO* 4.2 0.7 - - - +
97Z LEU* 3.0 27.3 + - - -
98Z LYS* 5.2 1.2 - - - +
99Z GLY 4.1 0.5 - - - +
100Z GLN* 1.3 82.3 - - - +
102Z LEU* 1.3 64.4 + - - +
226Z PRO* 4.2 11.9 - - - +
231Z PHE* 4.2 12.6 - - - -
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Residues in contact with LEU 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Z GLY* 4.5 4.3 - - - -
95Z ALA 3.7 3.1 - - - +
97Z LEU* 4.1 12.2 - - - +
101Z GLY* 1.3 74.7 - - - +
103Z GLY* 1.3 79.3 + - - +
104Z TRP* 4.1 22.4 - - + +
121Z ASP* 5.9 0.7 - - - +
221Z VAL* 5.6 2.9 - - + +
223Z ILE* 3.5 37.7 - - + +
226Z PRO* 4.2 14.6 - - + -
229Z VAL* 4.9 4.3 - - + -
231Z PHE* 3.5 32.8 - - + -
236Z THR* 5.8 0.9 - - - +
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Residues in contact with GLY 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Z GLY* 3.7 0.9 - - - -
95Z ALA* 2.9 36.8 + - - +
97Z LEU* 4.3 14.0 - - - +
102Z LEU* 1.3 81.9 - - - +
104Z TRP* 1.3 69.2 + - - -
121Z ASP* 3.7 13.0 - - - -
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Residues in contact with TRP 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Z LEU* 3.8 12.8 - - + -
93Z ILE 3.5 6.7 - - - -
94Z GLY* 3.5 27.4 - - - -
95Z ALA* 4.9 1.3 - - - -
102Z LEU* 4.1 24.5 - - + +
103Z GLY* 1.3 79.9 - - - -
105Z GLU* 1.3 61.5 + - - +
106Z THR* 4.0 2.6 - - - +
119Z PHE* 3.6 34.4 - + + -
121Z ASP* 3.2 20.8 + - + +
137Z CYS* 5.2 0.2 - - - -
139Z VAL* 5.0 8.1 - - + -
221Z VAL* 3.7 37.0 + - + +
223Z ILE* 4.7 1.1 - - + -
236Z THR* 4.2 5.6 - - - -
237Z PHE* 3.6 37.2 - - - -
238Z PHE* 3.4 40.7 - + + -
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Residues in contact with GLU 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Z LEU* 3.2 11.3 - - - +
93Z ILE* 2.8 46.8 + - + +
94Z GLY 4.8 1.1 - - - +
95Z ALA* 4.5 18.0 - - + +
103Z GLY 4.3 0.2 - - - -
104Z TRP* 1.3 71.6 - - - +
106Z THR* 1.3 74.2 + - - +
107Z THR* 3.5 11.3 + - - -
108Z LYS* 3.2 60.4 + - + +
111Z ALA* 3.4 3.3 - - + +
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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