Contacts of the strand formed by residues 105 - 112 (chain A) in PDB entry 3MWZ
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 LYS 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLU* 5.9 0.2 + - - -
23A MSE 4.5 12.6 - - + +
26A TYR* 3.5 54.1 + - + +
97A ILE* 4.1 12.8 - - + -
98A TYR 3.3 8.7 - - - +
99A ARG* 4.1 30.3 - - + +
103A GLY 3.7 2.7 + - - +
104A GLU* 1.3 75.6 - - - +
106A SER* 1.3 63.4 + - - +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MSE 4.3 26.1 + - - +
26A TYR* 3.5 10.8 - - - -
97A ILE* 3.3 6.7 - - - +
98A TYR* 2.9 35.6 + - - +
105A LYS* 1.3 77.1 - - - +
107A ILE* 1.3 65.6 + - - +
108A ASN* 5.2 0.2 - - - -
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Residues in contact with ILE 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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26A TYR* 3.6 26.0 + - + +
27A ALA* 3.8 22.7 - - + +
30A THR* 3.8 36.6 - - + -
31A TRP* 4.6 4.7 - - + +
34A GLN* 5.9 0.7 - - - +
95A THR* 3.7 10.3 - - - +
96A VAL 3.9 2.2 - - - -
97A ILE* 4.6 2.5 - - + +
106A SER* 1.3 74.1 - - - +
108A ASN* 1.3 62.1 + - - +
109A SER* 3.5 26.5 - - - +
110A PHE* 4.1 11.4 - - + -
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Residues in contact with ASN 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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1A MSE 3.0 28.1 + - - +
2A GLU* 3.0 36.0 + - - +
59A ASN* 5.8 0.9 - - - -
96A VAL* 2.8 28.4 + - + +
98A TYR* 4.5 8.5 - - + -
106A SER* 3.5 3.8 + - - -
107A ILE* 1.3 74.2 - - - +
109A SER* 1.3 66.2 + - - +
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Residues in contact with SER 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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94A THR 4.5 1.6 + - - -
95A THR* 2.8 28.2 + - - -
96A VAL* 3.0 35.9 + - - +
107A ILE* 3.4 5.7 - - - +
108A ASN* 1.3 85.2 + - - +
110A PHE* 1.3 55.3 + - - +
111A GLU* 4.1 20.5 + - - -
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Residues in contact with PHE 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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27A ALA* 3.7 17.0 - - + -
28A THR* 3.6 44.9 - - + -
31A TRP* 3.4 56.1 + + + -
64A LEU* 4.5 2.5 - - + -
66A VAL* 4.7 1.3 - - + -
93A CYS* 3.8 15.3 - - + -
94A THR 3.6 3.1 - - - -
95A THR* 3.4 30.1 - - + +
107A ILE* 4.1 9.2 - - + -
109A SER* 1.3 75.0 - - - +
111A GLU* 1.3 65.9 + - - +
112A CYS* 3.5 26.7 - - - -
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Residues in contact with GLU 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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93A CYS* 3.2 1.2 - - - -
94A THR* 2.8 46.6 + - - +
109A SER* 4.1 16.9 - - - -
110A PHE* 1.3 85.1 - - - +
112A CYS* 1.3 62.9 + - - +
113A ALA 4.2 0.3 + - - -
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Residues in contact with CYS 112 (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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31A TRP* 4.1 11.3 - - + -
91A ARG* 3.4 30.1 - - - +
92A THR 3.6 2.7 - - - -
93A CYS* 2.1 45.8 - - - -
110A PHE* 3.5 18.8 - - - -
111A GLU* 1.3 72.8 - - - +
113A ALA* 1.3 62.9 + - - +
114A ALA 3.9 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