Contacts of the strand formed by residues 92 - 97 (chain A) in PDB entry 1SXG
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 ASN 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 2.5 35.5 - - - +
61A THR 2.7 8.9 + - - +
62A THR* 3.5 21.9 - - - +
63A VAL* 2.6 30.8 + - - +
91A TYR* 1.3 73.2 + - - +
93A ILE* 1.3 68.9 + - - +
94A ILE* 5.9 0.7 - - + -
107D HIS* 3.7 14.8 + - - -
111D ASN* 2.8 35.3 + - + +
115D LYS* 5.3 3.6 - - - +
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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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63A VAL* 3.3 22.4 - - + -
65A VAL* 4.0 18.8 - - + -
79A ALA 6.0 0.4 - - - +
82A ILE* 5.3 0.4 - - + -
83A GLU* 4.3 38.8 - - + +
86A ALA* 3.1 35.9 - - + -
91A TYR* 4.1 4.3 - - + +
92A ASN* 1.3 103.3 - - - +
94A ILE* 1.3 71.3 + - - +
95A LEU* 4.2 8.9 + - + +
95D LEU 4.6 2.0 - - - +
96D SER* 4.5 12.8 + - - -
97D ASN* 5.9 0.9 - - - +
108D LEU* 5.8 1.7 - - - +
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Residues in contact with ILE 94 (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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62A THR* 3.9 5.6 - - - +
63A VAL 3.0 6.9 + - - +
64A GLY* 3.4 1.0 - - - -
65A VAL* 2.7 33.3 + - - +
92A ASN* 5.9 0.7 - - + -
93A ILE* 1.3 77.7 - - - +
95A LEU* 1.3 60.7 + - - +
96A SER* 5.4 0.2 - - - +
112A MET* 3.7 23.5 - - + +
115A LYS* 3.9 17.7 - - + -
117A VAL* 3.7 20.9 - - + -
94D ILE* 3.6 36.8 - - + -
95D LEU 4.5 2.2 - - - -
112D MET* 5.6 3.8 - - + -
115D LYS* 3.2 35.2 - - + +
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Residues in contact with LEU 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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65A VAL* 3.2 18.2 - - + +
67A ILE* 3.8 29.4 - - + -
79A ALA* 4.4 14.6 - - + -
93A ILE* 4.1 7.8 - - + -
94A ILE* 1.3 76.2 - - - +
96A SER* 1.3 73.4 + - - +
70D ILE* 3.8 22.4 - - + -
94D ILE* 3.7 3.3 - - - -
95D LEU* 2.8 59.5 + - + +
97D ASN* 3.7 26.5 - - - +
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Residues in contact with SER 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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65A VAL 2.8 5.9 + - - -
66A ILE* 3.3 15.8 - - - +
67A ILE* 3.1 24.1 + - - +
94A ILE 4.1 0.6 + - - -
95A LEU* 1.3 79.5 + - - +
97A ASN* 1.3 59.9 + - - +
108A LEU* 3.1 33.5 - - - +
111A ASN* 4.6 4.5 + - - -
112A MET* 4.5 11.1 - - - -
93D ILE 3.3 21.2 + - - -
94D ILE* 4.7 2.9 - - - +
95D LEU* 4.5 2.0 - - - -
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Residues in contact with ASN 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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67A ILE* 3.5 6.8 - - + +
68A PRO 3.3 1.7 - - - +
69A ASP* 3.0 29.8 + - - -
70A ILE* 3.2 31.5 - - + +
96A SER* 1.3 76.2 + - - +
98A SER* 1.3 64.6 + - - +
99A ASP* 3.3 27.2 + - - -
104A LYS* 3.3 24.8 + - - -
108A LEU* 4.1 5.6 - - - +
80D ARG* 4.2 3.0 - - - +
83D GLU* 3.5 29.7 + - - +
93D ILE 5.2 0.8 + - - -
95D LEU* 4.6 7.1 - - + +
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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