Contacts of the strand formed by residues 88 - 92 (chain B) in PDB entry 4MCA
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 VAL 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 3.4 2.8 - - - -
33B LEU* 3.4 7.0 - - + +
35B ILE* 3.8 29.8 - - + -
80B LEU* 3.8 24.9 - - + -
87B GLY* 1.3 79.0 - - - +
89B ILE* 1.3 62.6 + - - +
90B GLY 4.2 0.2 - - - -
100B ALA* 3.8 23.8 - - + +
103B ILE* 3.8 11.4 - - + -
104B ALA* 4.0 15.5 - - + -
109B LEU* 4.9 2.9 - - + -
110B PRO 3.0 9.1 + - - +
111B VAL* 3.2 9.6 - - + -
112B VAL 2.9 30.7 + - - +
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Residues in contact with ILE 89 (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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21B VAL* 4.9 2.9 - - + -
25B ALA* 4.8 4.5 - - + -
32B TYR* 3.4 42.2 - - + -
33B LEU 2.9 12.1 + - - +
34B VAL* 3.4 7.7 - - + +
35B ILE* 2.8 34.3 + - - +
48B LEU* 4.1 11.0 - - + -
52B LEU* 4.1 28.3 - - + -
88B VAL* 1.3 75.5 - - - +
90B GLY* 1.3 56.7 + - - +
91B VAL* 3.8 21.3 - - + -
112B VAL* 3.2 15.9 - - + +
114B ILE* 3.8 19.7 - - + -
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Residues in contact with GLY 90 (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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35B ILE* 3.6 5.8 - - - -
89B ILE* 1.3 72.7 - - - +
91B VAL* 1.3 61.8 + - - +
96B THR* 4.4 5.2 - - - -
97B LEU* 3.8 7.6 - - - +
100B ALA* 3.6 26.0 - - - +
112B VAL 2.9 9.7 + - - +
113B LEU* 3.7 4.5 - - - -
114B ILE* 2.8 28.6 + - - +
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Residues in contact with VAL 91 (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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18B LEU* 5.2 2.5 - - + -
34B VAL* 4.2 7.9 - - + -
35B ILE 2.9 15.6 + - - +
36B ALA* 3.7 7.2 - - + +
37B ASP 4.7 0.2 + - - -
40B VAL* 3.5 30.2 - - + +
41B MET* 6.4 0.2 - - - -
44B ALA* 4.3 13.2 - - + -
48B LEU* 4.0 16.2 - - + -
89B ILE* 3.8 19.3 - - + -
90B GLY* 1.3 78.7 - - - +
92B GLY* 1.3 60.8 + - - +
96B THR* 3.4 17.5 + - - +
114B ILE* 3.3 23.1 - - + +
116B THR* 4.0 9.6 - - + -
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Residues in contact with GLY 92 (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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40B VAL* 4.0 11.4 - - - -
91B VAL* 1.3 76.8 - - - +
93B GLY* 1.3 65.7 + - - +
96B THR* 4.6 2.5 - - - -
97B LEU* 3.8 7.0 - - - +
114B ILE 3.0 9.1 + - - -
115B PRO* 3.4 9.2 - - - +
116B THR* 3.3 37.6 + - - -
117B ILE* 4.7 0.7 + - - +
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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