Contacts of the strand formed by residues 92 - 97 (chain A) in PDB entry 2M3X
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 LEU 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE 4.6 0.2 - - - +
88A LEU* 4.3 0.7 - - - +
89A ASP* 3.0 41.6 + - + +
91A ASN* 1.3 91.8 - - - +
93A ILE* 1.3 67.6 + - - +
94A VAL* 4.2 4.4 + - + -
104A ILE* 4.3 15.5 - - + -
105A PHE 3.8 17.7 - - - +
106A ASN* 4.8 4.9 - - + +
112A LEU* 5.3 6.1 - - + -
125A VAL* 4.6 7.6 - - + -
127A ASN 4.0 4.3 - - - +
128A ASP* 3.6 31.9 - - - +
130A VAL* 3.5 27.6 - - + -
143A THR* 4.4 14.1 - - + -
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Residues in contact with ILE 93 (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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86A VAL* 5.4 0.9 - - + -
87A ILE 4.3 2.5 - - - +
88A LEU* 4.3 21.5 - - + -
89A ASP 5.5 0.7 - - - +
92A LEU* 1.3 79.4 - - - +
94A VAL* 1.3 64.1 + - - +
95A VAL* 4.4 16.6 - - + -
103A LEU 4.0 0.7 - - - +
104A ILE* 3.9 0.5 - - - -
105A PHE* 3.0 44.7 + - + +
106A ASN 3.5 23.1 - - - +
107A GLN* 4.4 4.3 - - - -
109A LEU* 5.0 8.5 - - + -
129F LEU* 5.0 7.6 - - + -
131F VAL* 6.3 0.2 - - + -
138F LEU* 4.8 11.9 - - + -
140F LEU* 3.5 39.7 - - + -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.9 1.7 - - - +
87A ILE* 3.1 41.3 + - + +
92A LEU* 4.9 3.8 - - + -
93A ILE* 1.3 79.5 - - - +
95A VAL* 1.3 69.2 + - - +
96A ILE* 4.7 4.6 - - + +
102A VAL* 4.0 25.1 - - + -
103A LEU 3.7 4.9 - - - +
104A ILE* 4.5 19.1 - - + -
123A VAL* 4.1 18.6 - - + -
125A VAL* 3.6 33.0 - - + -
130A VAL* 4.9 4.5 - - + -
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Residues in contact with VAL 95 (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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80A ILE* 4.4 21.3 - - + -
83A ILE* 3.9 27.6 - - + -
85A ASP 4.1 3.1 - - - +
86A VAL* 4.4 5.8 - - + +
93A ILE* 4.4 11.0 - - + -
94A VAL* 1.3 79.4 - - - +
96A ILE* 1.3 68.1 + - - +
97A THR* 4.2 5.1 + - + +
101A GLU 4.1 0.5 - - - +
102A VAL* 3.9 2.4 - - - +
103A LEU* 3.1 38.6 + - + +
105A PHE* 4.7 17.5 - - + -
138F LEU* 4.0 24.5 - - + -
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Residues in contact with ILE 96 (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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83A ILE* 4.1 2.4 - - - +
84A LYS* 3.1 38.2 + - - +
85A ASP* 3.1 37.2 + - + +
87A ILE* 4.9 8.5 - - + -
94A VAL* 4.7 8.1 - - + +
95A VAL* 1.3 80.0 - - - +
97A THR* 1.3 70.5 + - - +
100A ASN* 5.7 0.2 - - - -
101A GLU 3.8 6.3 - - - +
102A VAL* 4.6 5.2 - - + -
120A LEU* 4.0 21.5 - - + -
123A VAL* 3.5 36.8 - - + +
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Residues in contact with THR 97 (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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80A ILE* 4.4 22.0 - - + -
81A LYS 5.3 4.7 - - - +
82A GLY 3.9 11.7 - - - +
83A ILE* 5.1 0.9 - - - -
84A LYS* 4.1 6.3 - - - +
95A VAL* 4.7 4.3 - - + -
96A ILE* 1.3 84.1 - - - +
98A GLU* 1.3 65.1 + - - +
99A GLU* 2.9 18.0 + - - +
100A ASN* 3.0 14.6 + - - -
101A GLU* 3.2 30.9 + - - +
103A LEU* 4.5 19.3 - - + -
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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