Contacts of the strand formed by residues 91 - 96 (chain E) 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 GLU 91 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E HIS* 2.7 26.3 + - - -
90E GLY* 1.3 83.0 - - - +
92E GLN* 1.3 58.5 + - - +
143E SER* 3.3 34.2 + - - +
161E VAL* 5.0 7.6 - - - +
162E LYS 4.4 2.1 - - - +
163E VAL* 5.5 0.3 - - - -
164E ALA* 3.7 5.6 + - - +
243E LYS* 2.9 30.2 + - - +
244E ALA 3.2 10.1 - - - +
245E ARG* 2.7 48.8 + - + -
246E PHE* 4.1 2.9 - - - -
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Residues in contact with GLN 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E VAL* 3.9 13.4 - - + +
89E HIS* 2.8 29.7 + - - +
91E GLU* 1.3 74.6 - - - +
93E TYR* 1.3 75.4 + - - +
140E ASN* 3.2 28.9 + - - +
141E GLN 3.9 6.1 - - - +
142E PHE* 3.1 21.3 - - - -
217E LEU* 3.8 13.2 - - + -
220E PHE* 4.0 22.6 - - + -
242E VAL 3.9 0.6 - - - +
243E LYS* 3.2 8.4 - - - +
244E ALA* 3.0 31.1 + - - +
246E PHE* 4.1 15.3 - - + -
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Residues in contact with TYR 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E GLN* 1.3 84.5 + - - +
94E LEU* 1.3 60.7 + - - +
95E GLU* 2.9 46.3 + - + +
139E HIS* 4.0 13.9 - - - -
140E ASN* 3.2 5.2 - - - -
141E GLN* 2.9 47.5 + - + +
162E LYS* 3.7 52.9 + - + -
241E ALA* 3.8 13.3 - - + +
242E VAL 3.2 17.0 - - - -
243E LYS* 4.0 20.4 - - + +
285E TYR* 3.9 17.0 - - - -
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Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E PRO 3.4 27.4 - - - +
59E THR* 3.7 18.2 - - + -
61E GLY* 4.0 4.0 - - - -
62E VAL* 3.8 21.1 - - + +
92E GLN* 4.9 0.2 - - - +
93E TYR* 1.3 78.1 - - - +
95E GLU* 1.3 73.1 + - - +
96E LEU* 4.1 10.5 - - + -
138E CYS* 4.0 13.0 - - + -
139E HIS 3.3 8.5 - - - +
140E ASN* 3.4 27.4 - - - +
220E PHE* 5.3 0.4 - - + -
239E PHE* 5.7 1.5 - - + -
241E ALA* 3.0 5.9 - - - +
242E VAL* 2.9 43.2 + - + +
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Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E TYR* 2.9 31.5 + - + +
94E LEU* 1.3 75.1 - - - +
96E LEU* 1.3 67.1 + - - +
97E TYR* 3.4 46.1 + - + -
138E CYS* 3.2 6.2 - - - +
139E HIS* 2.9 35.2 + - + +
162E LYS* 4.7 5.9 + - - -
240E LYS* 3.3 13.5 - - + +
241E ALA* 3.9 4.5 - - + -
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E PRO* 3.4 50.3 - - + +
94E LEU* 4.1 13.5 - - + -
95E GLU* 1.3 76.3 - - - +
97E TYR* 1.3 66.5 + - - +
98E LYS* 3.0 12.0 + - - +
99E PRO* 5.2 2.5 - - + -
100E LEU* 4.0 20.6 - - + +
137E ILE 3.7 2.2 - - - -
138E CYS* 3.7 22.7 - - + -
236E VAL* 5.4 1.8 - - + +
239E PHE* 3.5 26.6 - - + +
240E LYS* 2.8 21.7 + - - +
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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