Contacts of the strand formed by residues 239 - 246 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K PRO* 3.4 36.6 - - + -
59K THR* 4.5 5.4 - - + -
94K LEU* 5.7 1.8 - - + -
96K LEU* 3.5 23.2 - - + +
224K ALA* 3.9 33.9 - - + -
228K LEU* 4.0 27.1 - - + +
235K ASP 3.9 0.8 + - - -
236K VAL 3.2 17.4 + - - +
237K SER 3.3 3.0 - - - +
238K ARG* 1.3 76.8 - - - +
240K LYS* 1.3 58.9 + - - +
241K ALA* 4.3 5.2 - - - -
242K VAL* 2.8 39.9 - - + -
286K VAL* 3.7 20.6 - - + -
288K LEU* 4.2 7.2 - - + -
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Residues in contact with LYS 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K GLU* 3.3 5.5 - - + +
96K LEU 2.7 39.3 + - - +
237K SER 5.3 2.9 - - - +
238K ARG 3.2 8.7 + - - +
239K PHE* 1.3 76.2 - - - +
241K ALA* 1.3 59.3 + - + +
287K ASP* 2.9 25.7 + - + +
288K LEU 4.4 9.1 + - - +
289K ALA* 4.2 24.4 - - + +
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Residues in contact with ALA 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K TYR* 3.8 15.7 - - + +
94K LEU 3.1 13.5 - - - +
95K GLU* 3.8 15.7 - - + -
96K LEU* 5.8 0.2 - - - -
239K PHE* 3.9 2.5 - - - -
240K LYS* 1.3 83.7 - - + +
242K VAL* 1.3 67.5 + - - +
285K TYR* 5.1 2.2 - - + -
286K VAL* 3.0 5.4 - - - +
287K ASP* 2.7 43.9 + - + +
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Residues in contact with VAL 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K THR* 4.7 4.7 - - + -
93K TYR* 3.3 7.4 - - - -
94K LEU* 2.8 34.9 + - + +
220K PHE* 3.0 41.1 - - + -
224K ALA* 5.1 3.6 - - + -
239K PHE* 2.8 46.4 - - + -
241K ALA* 1.3 73.1 - - - +
243K LYS* 1.3 62.1 + - - +
269K PHE* 5.3 4.3 - - + -
285K TYR* 3.2 14.1 - - - +
286K VAL* 4.1 4.3 - - + -
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Residues in contact with LYS 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K GLU* 3.0 37.0 + - - +
92K GLN 3.5 11.0 + - - +
93K TYR* 3.9 17.5 - - + +
141K GLN* 4.7 4.2 + - - -
143K SER* 5.3 1.4 - - - -
161K VAL* 4.6 4.8 - - - +
162K LYS 2.9 26.4 + - - +
163K VAL 3.6 14.1 - - - +
164K ALA* 3.7 25.8 - - - +
242K VAL* 1.3 76.6 - - - +
244K ALA* 1.3 73.3 + - - +
283K ASN 4.8 0.4 - - - +
284K ALA* 3.0 5.4 - - - +
285K TYR* 2.9 59.5 + - + +
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Residues in contact with ALA 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K GLU* 3.3 6.8 - - - +
92K GLN 3.0 30.9 + - - +
220K PHE* 3.6 31.0 - - + -
243K LYS* 1.3 82.5 - - - +
245K ARG* 1.3 61.1 + - - +
246K PHE* 5.1 4.9 - - + -
269K PHE* 4.4 2.5 - - + -
281K ILE* 3.8 12.3 - - + -
283K ASN 4.8 0.9 - - - -
284K ALA* 3.6 17.9 - - + +
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Residues in contact with ARG 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K GLY 3.8 3.4 - - - +
91K GLU* 2.7 35.4 + - + +
163K VAL* 5.8 1.8 - - - +
164K ALA* 3.5 25.8 - - + +
244K ALA* 1.3 74.6 - - - +
246K PHE* 1.3 74.7 + - - +
247K ALA* 6.0 0.4 - - + -
281K ILE* 3.3 5.4 - - - -
282K SER* 2.8 57.0 + - - +
283K ASN* 3.7 16.2 + - - +
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Residues in contact with PHE 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K HIS* 3.2 49.8 - + + +
90K GLY* 2.8 33.0 + - - +
91K GLU* 3.8 11.4 - - - -
92K GLN* 3.9 8.1 - - + -
216K GLY* 3.3 36.1 - - - -
217K LEU* 3.8 22.7 - - + -
220K PHE* 4.1 14.4 - + + -
244K ALA* 5.1 3.1 - - + -
245K ARG* 1.3 82.3 - - - +
247K ALA* 1.3 64.2 + - - +
280K VAL 3.7 3.4 - - - +
281K ILE* 4.2 19.3 - - + -
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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