Contacts of the strand formed by residues 250 - 258 (chain A) in PDB entry 1SLL
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 GLY 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ASP* 3.6 2.6 - - - +
94A ILE 2.9 34.0 + - - +
124A LYS 3.2 9.6 - - - -
126A THR* 3.3 19.1 + - - -
248A PHE* 3.6 6.8 - - - -
249A GLY* 1.3 73.8 - - - -
251A THR* 1.3 65.4 + - - -
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Residues in contact with THR 251 (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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91A ASN* 4.7 5.6 - - + +
92A VAL 3.3 9.6 - - - +
93A ASP* 2.7 26.2 + - - +
123A TYR* 3.2 5.4 - - - +
124A LYS* 2.8 60.7 + - - +
190A PHE* 4.0 14.3 - - + -
248A PHE* 3.7 1.4 - - - -
250A GLY* 1.3 75.8 - - - -
252A ILE* 1.3 77.2 + - - +
253A GLY* 3.5 4.7 + - - +
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Residues in contact with ILE 252 (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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89A LYS 5.3 0.4 - - - +
90A ASN 4.2 0.5 - - - -
91A ASN* 3.3 1.6 + - - -
92A VAL* 2.8 43.6 + - + +
94A ILE* 3.8 24.7 - - + -
121A LEU* 4.2 18.2 - - + -
122A SER 3.6 3.4 - - - +
123A TYR* 3.9 19.5 - - + -
134A LEU* 4.2 14.8 - - + +
235A LEU* 3.9 13.0 - - + -
248A PHE* 4.0 16.4 - - + -
251A THR* 1.3 71.5 - - - +
253A GLY* 1.3 65.6 + - - +
254A ASP* 3.8 24.2 - - - +
255A ILE* 4.2 17.0 - - + -
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Residues in contact with GLY 253 (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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90A ASN* 3.3 5.2 - - - +
91A ASN* 2.7 33.8 + - - +
122A SER* 2.7 19.5 + - - -
190A PHE* 3.7 20.7 - - - -
251A THR* 3.5 8.6 + - - -
252A ILE* 1.3 70.9 - - - +
254A ASP* 1.3 59.6 + - - +
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Residues in contact with ASP 254 (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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88A GLU* 3.2 13.4 - - - +
89A LYS 3.1 11.8 - - - +
90A ASN* 2.7 40.5 + - - +
120A ILE* 5.1 1.4 - - - +
121A LEU* 3.1 6.6 - - - +
122A SER* 2.9 36.4 + - - +
252A ILE* 3.3 3.8 - - - +
253A GLY* 1.3 75.6 - - - +
255A ILE* 1.3 63.4 + - - +
256A LYS* 3.7 26.0 - - - +
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Residues in contact with ILE 255 (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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87A MET* 6.0 2.5 - - + -
88A GLU* 3.1 10.0 - - - +
89A LYS* 3.0 44.5 + - + +
102A LEU* 4.9 4.7 - - + -
119A ILE* 4.2 6.3 - - + -
120A ILE 3.2 11.0 - - - +
121A LEU* 3.9 11.2 - - + -
135A PHE* 3.4 44.2 - - + -
235A LEU* 3.8 17.3 - - + -
252A ILE* 4.2 12.1 - - + -
254A ASP* 1.3 76.6 - - - +
256A LYS* 1.3 65.6 + - - +
257A VAL* 4.1 15.0 - - + -
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Residues in contact with LYS 256 (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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85A ILE* 3.7 20.4 - - + +
87A MET 3.6 4.9 - - - +
88A GLU* 3.1 37.1 + - + +
118A THR 3.7 0.9 - - - +
119A ILE* 3.5 3.5 - - - +
120A ILE* 2.9 44.9 + - + +
254A ASP* 3.7 18.8 - - - +
255A ILE* 1.3 75.0 - - - +
257A VAL* 1.3 61.3 + - - +
258A TYR* 3.3 32.4 + - + +
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Residues in contact with VAL 257 (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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85A ILE* 3.5 3.2 - - - +
86A LEU* 2.8 34.3 + - + +
87A MET* 3.0 31.4 + - + +
111A VAL* 4.0 14.1 - - + -
114A MET* 3.6 36.6 - - + -
118A THR 3.4 3.1 - - - -
119A ILE* 4.2 12.8 - - + -
135A PHE* 4.2 14.8 - - + -
255A ILE* 4.1 23.8 - - + -
256A LYS* 1.3 76.1 - - - +
258A TYR* 1.3 55.8 + - - +
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Residues in contact with TYR 258 (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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84A GLY* 3.3 6.5 - - - -
85A ILE* 3.6 31.9 - - + +
86A LEU* 4.6 0.7 - - - -
114A MET* 3.1 8.3 - - - +
117A GLY* 3.1 3.8 - - - -
118A THR* 2.8 41.1 + - - +
120A ILE* 3.9 12.7 - - + +
256A LYS* 3.3 46.7 + - + +
257A VAL* 1.3 76.8 - - - +
259A SER* 1.3 59.9 + - - +
260A ASN* 3.6 28.0 - - - +
262A LEU* 4.0 35.2 - - + +
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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