Contacts of the helix formed by residues 91 - 99 (chain A) in PDB entry 1SL1
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 THR 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.7 24.9 - - + -
58A PHE 2.9 6.5 + - - -
59A HIS* 2.8 37.9 + - - +
89A ILE* 5.1 0.4 - - + -
90A ASP* 1.3 68.9 - - - +
92A LEU* 1.3 59.5 + - - +
94A LEU* 3.8 6.5 - - + -
95A SER* 2.8 33.8 + - - -
178A THR* 3.6 11.2 - - + +
181A LEU* 3.8 12.3 - - - +
182A LEU* 3.9 33.7 - - + -
185A LEU* 3.6 4.6 - - + +
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Residues in contact with LEU 92 (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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59A HIS* 3.4 28.9 + - + +
60A ASN* 3.4 34.8 - - + +
63A LYS* 6.1 0.7 - - + -
90A ASP* 2.8 12.9 + - - +
91A THR* 1.3 78.8 - - - +
93A VAL* 1.3 65.1 + - + +
95A SER* 3.2 7.4 + - - -
96A ARG* 3.0 68.6 + - + +
104A ASP* 4.3 10.8 - - + +
106A ASP* 5.3 1.3 - - - +
107A MET* 4.3 14.1 - - + +
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Residues in contact with VAL 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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62A HIS* 4.8 3.4 - - + -
90A ASP* 3.1 34.0 + - + +
92A LEU* 1.3 80.3 - - + +
94A LEU* 1.3 62.2 + - - +
96A ARG* 3.4 8.8 + - - +
97A LEU* 3.2 19.9 + - - +
217A GLU* 3.5 45.0 - - + +
218A HIS* 4.1 12.8 - - + +
221A ALA* 3.6 23.3 - - + -
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Residues in contact with LEU 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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89A ILE* 4.5 16.6 - - + -
90A ASP 2.9 11.2 + - - +
91A THR* 3.8 1.6 - - - +
93A VAL* 1.3 78.0 - - - +
95A SER* 1.3 56.9 + - - +
97A LEU* 3.1 11.0 + - + +
98A ILE* 2.9 40.1 + - + +
182A LEU* 4.6 12.1 - - + -
185A LEU* 3.6 32.1 - - + -
186A LEU* 4.8 2.0 - - + -
192A PHE* 4.0 32.5 - - + -
206A PHE* 5.1 2.7 - - + -
214A VAL* 4.1 22.2 - - + -
218A HIS* 3.9 15.7 - - + -
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Residues in contact with SER 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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59A HIS* 5.6 0.7 - - - -
91A THR 2.8 23.8 + - - -
92A LEU* 3.5 10.9 - - - -
94A LEU* 1.3 76.4 - - - +
96A ARG* 1.3 57.9 + - - +
99A HIS* 2.7 43.6 + - - +
126A GLU* 5.0 6.0 + - - -
129A GLY* 5.8 1.3 - - - -
181A LEU* 3.6 17.8 - - - +
185A LEU* 3.5 22.7 - - - +
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Residues in contact with ARG 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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63A LYS* 5.6 6.9 - - - +
92A LEU* 3.0 48.9 + - + +
93A VAL* 3.8 7.6 - - - +
94A LEU 3.3 0.2 - - - -
95A SER* 1.3 78.0 - - - +
97A LEU* 1.3 57.6 + - - +
99A HIS 4.9 2.0 - - - -
100A SER* 3.2 19.7 - - - +
104A ASP* 2.8 42.0 + - - +
106A ASP* 3.1 31.9 + - - +
420A VAL 5.3 0.6 + - - -
421A ASN* 3.2 45.6 + - - +
422A PRO* 4.5 8.1 - - - +
423A ASN* 2.9 36.2 + - + +
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Residues in contact with LEU 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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93A VAL 3.2 11.9 + - - +
94A LEU* 3.1 16.0 + - + +
95A SER 3.1 0.2 - - - -
96A ARG* 1.3 79.7 - - - +
98A ILE* 1.3 65.3 + - + +
100A SER* 3.5 14.0 + - - -
191A TYR* 3.9 23.6 + - + -
213A ALA* 3.6 33.4 - - + +
214A VAL* 3.9 13.0 - - + +
217A GLU* 4.0 11.7 - - + -
423A ASN* 3.9 4.2 - - - +
599A ARG* 3.5 53.8 - - + +
600A LYS 5.2 0.7 - - - +
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Residues in contact with ILE 98 (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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94A LEU* 2.9 22.2 + - + +
97A LEU* 1.3 79.9 - - + +
99A HIS* 1.3 76.2 + - + +
100A SER* 3.4 3.2 + - - -
101A ASN* 4.4 2.9 - - - +
185A LEU* 3.5 45.3 - - + +
188A ASP* 3.5 25.1 - - + +
191A TYR* 3.9 37.7 + - + -
192A PHE* 4.3 13.5 - - + -
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Residues in contact with HIS 99 (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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95A SER* 2.7 28.2 + - - +
96A ARG* 5.0 1.2 - - - -
98A ILE* 1.3 83.2 + - + +
100A SER* 1.3 56.1 + - - +
101A ASN* 3.0 15.0 + - - -
102A LEU* 3.0 48.1 + - + +
126A GLU* 4.3 24.3 - - + +
181A LEU* 5.8 0.2 - - - +
184A LYS* 4.7 16.2 - - - +
185A LEU* 3.8 29.5 - - + +
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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