Contacts of the strand formed by residues 88 - 96 (chain C) in PDB entry 1S9C
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 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ALA 6.2 0.2 - - - +
86C LYS 5.2 3.4 - - - +
87C VAL* 1.3 83.3 - - - +
89C HIS* 1.3 63.1 + - - +
90C GLY* 3.7 0.4 - - - -
144C LEU* 3.4 9.0 - - - +
145C PHE* 2.6 66.2 + - + +
146C LEU 6.4 0.2 - - - -
197C LEU* 6.1 5.4 - - + -
209C PHE* 6.5 1.6 - - + -
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Residues in contact with HIS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C MET* 4.5 13.7 - - + +
88C LEU* 1.3 73.2 - - - +
90C GLY* 1.3 57.9 + - - +
91C GLU 2.9 23.2 + - - -
92C GLN* 2.8 28.5 + - - -
142C PHE* 4.0 10.2 - + - -
143C SER 3.9 4.0 - - - -
144C LEU* 4.0 15.9 - - + -
216C GLY* 6.0 1.5 - - - -
217C LEU* 3.6 37.8 + - + +
246C PHE* 3.2 35.9 - + + +
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.5 5.1 + - - -
89C HIS* 1.3 73.9 - - - +
91C GLU* 1.3 65.1 + - - +
143C SER* 2.9 17.3 + - - -
145C PHE* 4.4 10.0 - - - +
245C ARG* 3.7 2.1 - - - +
246C PHE* 2.8 34.5 + - - +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C HIS* 2.9 20.7 + - - -
90C GLY* 1.3 83.3 - - - +
92C GLN* 1.3 62.0 + - - +
141C GLN 4.7 0.2 - - - -
143C SER* 3.2 35.8 + - - +
161C VAL* 4.7 9.9 - - - +
162C LYS 4.6 1.4 - - - +
164C ALA* 3.8 4.2 + - - +
243C LYS* 3.1 30.4 + - - +
244C ALA 3.3 8.3 - - - +
245C ARG* 2.6 51.0 + - + +
246C PHE* 4.1 2.5 - - - -
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Residues in contact with GLN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C VAL* 4.0 9.6 - - + +
89C HIS* 2.8 32.4 + - - +
91C GLU* 1.3 75.0 - - - +
93C TYR* 1.3 74.3 + - - +
140C ASN* 3.2 26.9 + - - +
141C GLN 3.8 4.4 - - - +
142C PHE* 3.0 32.9 - - - -
217C LEU* 3.8 13.9 - - + -
220C PHE* 4.0 22.5 - - + -
242C VAL 4.1 0.6 - - - +
243C LYS* 3.3 7.0 - - - +
244C ALA 2.9 31.3 + - - +
246C PHE* 4.0 15.2 - - + -
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Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLN* 1.3 84.0 + - - +
94C LEU* 1.3 62.1 + - - +
95C GLU* 2.9 45.8 + - + +
139C HIS* 4.1 13.9 - + - -
140C ASN* 3.2 5.2 - - - -
141C GLN* 2.8 47.3 + - + +
162C LYS* 3.6 51.3 + - + -
241C ALA* 3.9 13.2 - - + +
242C VAL 3.3 16.6 - - - -
243C LYS* 3.9 21.1 - - + +
285C TYR* 3.9 17.3 - - - -
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PRO 3.4 27.1 - - - +
59C THR* 3.7 19.1 - - + -
61C GLY* 4.0 3.8 - - - -
62C VAL* 3.8 20.9 - - + +
92C GLN* 4.9 0.2 - - - +
93C TYR* 1.3 80.2 - - - +
95C GLU* 1.3 73.2 + - - +
96C LEU* 4.1 10.8 - - + -
138C CYS* 4.0 12.6 - - + -
139C HIS 3.4 8.7 - - - +
140C ASN* 3.3 27.6 - - - +
220C PHE* 5.2 0.4 - - + -
239C PHE* 5.9 1.1 - - + -
241C ALA* 3.1 5.2 - - - +
242C VAL* 2.8 45.3 + - + +
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C TYR* 2.9 32.5 + - + +
94C LEU* 1.3 74.7 - - - +
96C LEU* 1.3 66.8 + - - +
97C TYR* 3.5 44.7 + - + -
138C CYS* 3.2 6.8 - - - +
139C HIS* 2.9 34.8 + - + +
162C LYS* 4.6 6.6 + - - -
240C LYS* 3.4 12.8 - - + +
241C ALA* 3.8 5.6 - - + -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PRO* 3.4 51.4 - - + +
94C LEU* 4.1 12.3 - - + -
95C GLU* 1.3 75.4 - - - +
97C TYR* 1.3 65.3 + - - +
98C LYS* 3.1 12.8 + - - +
99C PRO* 5.4 2.7 - - + -
100C LEU* 4.0 21.3 - - + +
137C ILE 3.7 2.2 - - - -
138C CYS* 3.6 22.7 - - + -
236C VAL* 5.5 2.2 - - + +
239C PHE* 3.5 23.9 - - + +
240C LYS* 2.7 25.6 + - - +
241C ALA* 5.8 0.2 - - - -
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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