Contacts of the strand formed by residues 239 - 246 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D PRO* 3.4 33.7 - - + -
59D THR* 4.6 4.9 - - + -
94D LEU* 5.8 2.7 - - + -
96D LEU* 3.4 24.2 - - + +
224D ALA* 3.9 32.5 - - + -
228D LEU* 4.0 28.7 - - + +
235D ASP 3.9 1.0 + - - -
236D VAL 3.2 17.7 + - - +
237D SER 3.2 2.5 - - - +
238D ARG* 1.3 75.8 - - - +
240D LYS* 1.3 58.2 + - - +
241D ALA* 4.3 5.8 - - - -
242D VAL* 2.9 39.5 - - + -
286D VAL* 3.7 22.4 - - + -
288D LEU* 4.2 6.9 - - + +
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Residues in contact with LYS 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLU* 3.4 5.7 - - + +
96D LEU* 2.7 40.4 + - - +
237D SER 5.4 2.7 - - - +
238D ARG 3.2 8.0 + - - +
239D PHE* 1.3 75.3 - - - +
241D ALA* 1.3 58.8 + - + +
287D ASP* 3.0 26.2 + - + +
288D LEU 4.4 6.7 + - - +
289D ALA* 3.5 29.2 - - + +
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Residues in contact with ALA 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D TYR* 3.9 16.6 - - + +
94D LEU 3.0 17.5 - - - +
95D GLU* 3.7 15.5 - - + -
96D LEU* 5.8 0.4 - - - -
239D PHE* 3.9 3.0 - - - -
240D LYS* 1.3 82.8 - - + +
242D VAL* 1.3 65.1 + - - +
285D TYR* 5.1 2.0 - - + -
286D VAL* 3.0 5.5 - - - +
287D ASP* 2.7 44.2 + - + +
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D THR* 4.8 4.9 - - + -
93D TYR* 3.3 7.0 - - - -
94D LEU* 2.9 38.4 + - + +
220D PHE* 3.1 40.2 - - + -
224D ALA* 4.9 4.3 - - + -
239D PHE* 2.9 44.2 - - + -
241D ALA* 1.3 72.3 - - - +
243D LYS* 1.3 61.0 + - - +
269D PHE* 5.3 4.5 - - + -
285D TYR* 3.2 13.7 - - - +
286D VAL* 3.9 5.6 - - + -
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLU* 3.1 39.4 + - - +
92D GLN 3.2 19.6 + - - +
93D TYR* 3.9 14.8 - - + +
141D GLN* 4.9 5.7 + - - -
143D SER* 5.0 2.4 - - - -
161D VAL* 5.4 0.4 - - - +
162D LYS* 2.9 28.3 + - - +
163D VAL 3.5 15.0 - - - +
164D ALA* 3.6 26.9 - - - +
242D VAL* 1.3 76.5 - - - +
244D ALA* 1.3 65.2 + - - +
269D PHE* 4.4 0.2 - - - -
283D ASN 4.8 0.7 - - - +
284D ALA* 2.9 5.4 - - - +
285D TYR* 2.8 59.1 + - + +
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Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLU* 3.2 6.1 - - - +
92D GLN* 2.9 32.9 + - - +
220D PHE* 3.6 31.4 - - + -
243D LYS* 1.3 81.6 - - - +
245D ARG* 1.3 60.4 + - - +
246D PHE* 4.2 4.6 - - + -
269D PHE* 4.4 2.9 - - + -
281D ILE* 3.8 12.1 - - + -
283D ASN 4.8 1.1 - - - -
284D ALA* 3.5 18.4 - - + +
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Residues in contact with ARG 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLY 3.5 10.8 - - - +
91D GLU* 2.6 31.5 + - + +
163D VAL* 5.7 3.0 - - - +
164D ALA* 3.5 25.1 - - + +
244D ALA* 1.3 75.2 - - - +
246D PHE* 1.3 71.5 + - - +
247D ALA* 6.1 0.2 - - + -
281D ILE* 3.3 6.0 - - - +
282D SER* 2.8 57.3 + - - +
283D ASN* 3.9 15.0 - - - +
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Residues in contact with PHE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LYS* 5.8 1.4 + - - -
89D HIS* 3.6 50.3 - + + +
90D GLY* 2.8 24.3 + - - +
91D GLU* 4.1 2.2 - - - -
92D GLN* 4.0 15.7 - - + -
216D GLY* 3.4 35.2 - - - -
217D LEU* 3.8 23.6 - - + -
220D PHE* 4.1 15.0 - + + -
244D ALA* 4.9 3.4 - - + -
245D ARG* 1.3 83.8 - - - +
247D ALA* 1.3 64.1 + - - +
280D VAL 3.8 3.8 - - - +
281D ILE* 4.3 18.8 - - + -
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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