Contacts of the strand formed by residues 111 - 118 (chain I) in PDB entry 1MWA
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 ARG 111 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I GLY 4.6 0.3 - - - +
101I CYS* 4.4 0.9 - - - -
102I GLU* 3.5 42.3 + - - +
109I LEU* 3.5 11.9 - - - +
110I LEU* 1.3 85.2 - - + +
112I GLY* 1.3 70.2 + - - +
113I TYR* 3.3 40.0 + - - +
115I GLN* 5.7 1.6 - - - +
128I GLU* 4.4 29.4 - - + -
130I LEU* 6.0 1.1 - - - -
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Residues in contact with GLY 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I GLY 4.3 7.4 - - - -
101I CYS* 5.4 0.2 - - - -
109I LEU* 4.3 13.1 - - - +
111I ARG* 1.3 79.9 - - - +
113I TYR* 1.3 61.1 + - - -
126I LEU* 4.7 3.6 - - - +
127I ASN 4.1 9.4 - - - +
128I GLU* 5.5 0.2 - - - -
130I LEU* 3.5 34.3 - - - +
160I LEU* 4.6 10.5 - - - -
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Residues in contact with TYR 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I SER* 4.7 1.6 - - - -
6I ARG* 2.9 42.3 + - + +
98I ILE* 4.0 16.0 - - + +
99I SER* 4.1 2.4 - - - -
100I GLY* 3.5 43.7 + - - +
101I CYS* 5.0 0.2 - - - -
102I GLU* 3.1 39.0 + - + +
111I ARG* 3.3 36.6 - - + +
112I GLY* 1.3 74.9 - - - -
114I GLN* 1.3 66.7 + - - +
115I GLN* 3.7 19.5 - - - +
126I LEU* 5.1 5.6 - - - +
160I LEU* 4.3 8.1 - - - +
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Residues in contact with GLN 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I ILE 3.3 7.8 + - - +
99I SER* 4.7 9.9 - - - -
113I TYR* 1.3 81.4 - - - +
115I GLN* 1.3 71.8 + - - +
116I TYR* 3.2 30.6 + - + -
124I ILE* 3.7 9.5 + - - +
125I ALA* 3.3 1.9 - - - -
126I LEU* 3.3 24.8 + - + +
133I TRP* 3.3 26.7 - - - -
147I TRP* 3.5 17.8 - - - -
156I LEU* 3.8 34.7 - - + +
160I LEU* 5.4 0.7 - - + -
5Q PHE* 6.2 0.9 - - + -
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Residues in contact with GLN 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I VAL* 4.1 0.3 - - - +
98I ILE* 2.9 49.1 + - + +
111I ARG* 5.7 1.6 - - - +
113I TYR* 3.7 29.3 - - - +
114I GLN* 1.3 82.7 - - - +
116I TYR* 1.3 70.6 + - - +
122I ASP* 5.2 4.6 - - + +
124I ILE 3.7 8.7 - - - +
125I ALA* 3.9 19.1 - - + -
60M TRP* 3.4 30.5 - - + -
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Residues in contact with TYR 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I PHE* 3.8 32.1 - + - -
81I LEU* 6.2 2.2 - - + -
95I ILE* 4.7 7.0 - - + -
96I GLN 3.4 4.5 - - - -
97I VAL* 3.9 16.6 - - + -
114I GLN* 3.2 33.8 + - + -
115I GLN* 1.3 82.9 - - - +
117I ALA* 1.3 60.9 + - - +
118I TYR 4.0 0.4 - - - -
121I CYS 3.2 0.3 - - - +
122I ASP* 3.0 8.1 - - - -
123I TYR* 2.9 49.9 + + + +
124I ILE* 4.3 5.4 + - + -
147I TRP* 4.5 14.3 - + - -
60M TRP* 4.0 3.4 - - - -
3Q TYR* 5.7 0.3 - - - -
5Q PHE* 2.8 34.9 - + + +
6Q TYR 4.8 5.7 + - - -
8Q VAL* 5.1 16.2 - - + -
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Residues in contact with ALA 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I THR 3.8 0.2 - - - +
95I ILE* 3.1 13.8 - - - +
96I GLN* 2.6 69.8 + - + +
116I TYR* 1.3 74.4 - - - +
118I TYR* 1.3 59.7 + - - +
119I ASP 3.9 0.3 + - - -
121I CYS 3.2 8.5 - - - +
60M TRP* 3.4 26.2 - - + -
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Residues in contact with TYR 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I LEU* 5.6 3.4 - - + -
81I LEU* 4.5 25.4 - - + -
82I LEU* 4.6 3.4 - - + -
85I TYR* 3.3 40.7 - + - +
87I GLN* 2.7 44.1 + - - +
93I HIS* 3.5 14.9 + + + -
94I THR 4.0 8.5 - - - -
95I ILE* 5.1 0.7 - - - +
116I TYR* 3.9 1.7 + - + +
117I ALA* 1.3 70.5 - - - +
119I ASP* 1.3 83.2 + - + +
120I GLY 2.6 15.6 + - - -
121I CYS* 2.7 29.7 + - + +
122I ASP 5.5 1.1 - - - +
123I TYR* 5.1 11.0 - - + -
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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