Contacts of the strand formed by residues 92 - 97 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS* 6.1 4.7 - - - +
107A HIS* 3.5 30.6 + - - -
108A LEU* 5.3 5.3 - - - +
111A ASN* 3.3 25.6 + - - +
60D THR* 4.9 6.4 - - - +
61D THR 3.3 14.4 + - - +
62D THR* 3.5 21.1 - - - +
63D VAL* 2.9 26.9 + - - +
90D LYS 5.7 0.5 - - - +
91D TYR* 1.3 77.5 + - - +
93D ILE* 1.3 67.0 + - - +
94D ILE* 4.7 2.2 - - + -
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Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A SER* 3.3 19.2 + - - -
97A ASN 5.2 0.2 + - - -
104A LYS* 6.4 0.2 - - - +
63D VAL* 3.2 35.9 - - + +
65D VAL* 3.8 6.7 - - + -
82D ILE* 4.1 20.0 - - + -
83D GLU* 3.8 31.7 - - + +
86D ALA* 3.4 32.8 - - + -
91D TYR 4.0 0.6 + - - +
92D ASN* 1.3 74.3 - - - +
94D ILE* 1.3 73.9 + - - +
95D LEU* 3.4 28.3 - - + -
302D MET* 4.2 2.0 - - - -
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 3.6 35.4 - - + -
95A LEU 3.7 3.8 - - - -
96A SER* 4.7 2.7 - - - +
111A ASN* 3.9 23.8 - - - +
115A LYS* 4.4 13.0 - - + -
62D THR* 3.6 23.6 - - - +
63D VAL 3.0 7.0 + - - +
64D GLY* 4.3 7.2 - - - -
65D VAL 2.8 27.5 + - - +
92D ASN* 4.7 0.4 - - + -
93D ILE* 1.3 89.8 - - - +
95D LEU* 1.3 71.0 + - - +
96D SER* 5.2 0.2 - - - +
112D MET* 3.5 27.8 - - + +
117D VAL* 5.3 2.7 - - + -
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Residues in contact with LEU 95 (chain D).
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* 6.1 0.9 - - + -
70A ILE* 5.7 1.8 - - + -
93A ILE* 4.6 1.6 - - - +
94A ILE* 4.4 2.3 - - - -
95A LEU* 2.8 64.8 + - + +
96A SER* 4.5 7.6 - - - -
97A ASN* 4.6 10.8 - - + +
65D VAL* 3.5 25.8 - - + +
67D ILE* 5.7 4.3 - - + -
70D ILE* 4.4 25.6 - - + -
79D ALA* 5.5 7.9 - - + -
82D ILE* 5.9 1.1 - - + -
83D GLU* 4.7 7.0 - - + +
93D ILE* 3.4 28.5 - - + -
94D ILE* 1.3 78.9 - - - +
96D SER* 1.3 64.8 + - - +
97D ASN* 5.6 0.7 - - - +
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Residues in contact with SER 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE 4.5 9.3 + - - -
65D VAL 2.9 5.6 + - - -
66D ILE* 3.3 31.3 - - - +
67D ILE* 3.0 29.3 + - - +
95D LEU* 1.3 76.3 + - - +
97D ASN* 1.3 64.6 + - - +
108D LEU* 3.5 24.1 + - - +
111D ASN* 5.9 0.7 - - - +
112D MET* 4.0 14.7 - - - +
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA 5.9 0.6 + - - -
80A ARG* 2.9 31.2 - - - +
83A GLU* 3.1 27.6 + - - +
93A ILE* 5.9 1.0 - - - +
95A LEU* 3.7 27.7 - - - +
67D ILE* 3.4 3.6 - - - +
69D ASP* 3.4 4.5 + - - -
70D ILE* 2.8 39.2 + - - +
95D LEU* 5.9 0.7 - - - -
96D SER* 1.3 76.0 - - - +
98D SER* 1.3 60.2 + - - +
104D LYS* 2.9 27.2 - - - -
108D LEU* 3.1 6.3 - - - +
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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