Contacts of the strand formed by residues 239 - 246 (chain I) 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 PHE 239 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I PRO* 3.5 36.8 - - + -
59I THR* 4.4 5.2 - - + -
94I LEU* 5.7 2.2 - - + -
96I LEU* 3.5 23.8 - - + +
224I ALA* 3.8 33.9 - - + -
228I LEU* 4.0 25.3 - - + +
235I ASP 3.9 1.0 + - - -
236I VAL 3.2 17.0 + - - +
237I SER 3.2 3.4 - - - +
238I ARG* 1.3 75.7 - - - +
240I LYS* 1.3 61.2 + - - +
241I ALA* 4.3 5.2 - - - -
242I VAL* 2.9 38.8 - - + -
286I VAL* 3.8 20.6 - - + -
288I LEU* 4.2 7.2 - - + -
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Residues in contact with LYS 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I GLU* 3.5 4.4 - - + +
96I LEU* 2.7 40.7 + - - +
237I SER 5.3 2.7 - - - +
238I ARG 3.3 7.2 + - - +
239I PHE* 1.3 76.0 - - - +
241I ALA* 1.3 57.9 + - + +
287I ASP* 3.0 25.9 + - + +
288I LEU 4.5 4.2 + - - +
289I ALA* 3.5 33.3 - - + +
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Residues in contact with ALA 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I TYR* 4.0 13.0 - - + +
94I LEU 3.2 13.9 - - - +
95I GLU* 3.7 17.7 - - + -
96I LEU* 5.7 0.2 - - - -
239I PHE* 3.8 3.2 - - - -
240I LYS* 1.3 84.7 - - + +
242I VAL* 1.3 66.0 + - - +
285I TYR* 5.1 2.9 - - + +
286I VAL* 3.0 5.7 - - - +
287I ASP* 2.7 43.3 + - + +
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Residues in contact with VAL 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I THR* 4.8 4.9 - - + -
93I TYR* 3.4 7.2 - - - -
94I LEU* 2.8 37.3 + - + +
220I PHE* 3.2 37.9 - - + -
224I ALA* 5.0 4.7 - - + -
239I PHE* 2.9 44.6 - - + -
241I ALA* 1.3 73.6 - - - +
243I LYS* 1.3 61.7 + - - +
269I PHE* 5.3 4.9 - - + -
285I TYR* 3.2 13.0 - - - +
286I VAL* 4.0 5.4 - - + +
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Residues in contact with LYS 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I GLU* 3.3 35.6 + - - +
92I GLN 3.5 11.1 + - - +
93I TYR* 3.8 20.3 - - + +
141I GLN* 4.8 4.6 + - - -
143I SER* 5.4 1.2 - - - -
161I VAL* 4.7 4.2 - - - +
162I LYS 3.0 27.3 + - - +
163I VAL 3.7 14.1 - - - +
164I ALA* 3.8 23.8 - - - +
242I VAL* 1.3 76.7 - - - +
244I ALA* 1.3 74.5 + - - +
269I PHE* 4.4 0.3 - - - -
283I ASN 4.8 0.7 - - - +
284I ALA* 3.0 4.9 - - - +
285I TYR* 2.9 58.5 + - + +
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Residues in contact with ALA 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I GLU* 3.4 6.1 - - - +
92I GLN 3.0 32.2 + - - +
164I ALA* 5.7 0.2 - - - -
220I PHE* 3.6 32.8 - - + -
243I LYS* 1.3 82.8 - - - +
245I ARG* 1.3 61.6 + - - +
246I PHE* 4.2 3.7 - - + -
269I PHE* 4.5 2.9 - - + -
281I ILE* 3.8 11.9 - - + -
283I ASN 4.8 0.9 - - - -
284I ALA* 3.6 17.3 - - + +
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Residues in contact with ARG 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I GLY 3.9 3.1 - - - +
91I GLU* 2.6 34.8 + - + +
163I VAL* 5.7 2.2 - - - +
164I ALA* 3.4 28.8 - - + +
244I ALA* 1.3 75.7 - - - +
246I PHE* 1.3 74.8 + - - +
247I ALA* 6.0 0.2 - - + -
281I ILE* 3.3 5.8 - - - -
282I SER* 2.8 57.5 + - - +
283I ASN* 3.8 15.0 + - - +
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Residues in contact with PHE 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I HIS* 3.1 53.6 - + + +
90I GLY* 2.8 31.8 + - - +
91I GLU* 3.7 10.3 - - - -
92I GLN* 3.8 7.4 - - + -
216I GLY* 3.2 42.6 - - - -
217I LEU* 3.9 17.7 - - + -
219I THR* 6.1 0.2 - - - -
220I PHE* 4.1 15.9 - + + -
244I ALA* 4.9 2.9 - - + -
245I ARG* 1.3 84.0 - - - +
247I ALA* 1.3 62.3 + - - +
280I VAL 3.7 2.9 - - - +
281I ILE* 4.2 17.3 - - + -
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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