Contacts of the strand formed by residues 88 - 96 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85F ALA 5.1 0.7 - - - +
86F LYS 3.6 12.3 - - - +
87F VAL* 1.3 97.7 - - - +
89F HIS* 1.3 62.1 + - - +
90F GLY* 3.3 2.5 + - - -
144F LEU* 3.1 6.7 - - - -
145F PHE* 2.6 53.8 + - + +
147F VAL* 4.7 22.2 - - + -
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Residues in contact with HIS 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F MET* 4.1 16.9 - - + +
88F LEU* 1.3 72.5 - - - +
90F GLY* 1.3 57.8 + - - +
91F GLU 2.7 32.9 + - - -
92F GLN* 2.8 24.5 + - - -
142F PHE* 3.8 12.9 - + - -
143F SER 3.8 5.8 - - - -
144F LEU* 4.4 14.8 - - + -
217F LEU* 3.9 22.8 - - + +
246F PHE* 3.6 30.5 - + + +
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Residues in contact with GLY 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F LEU* 3.3 5.4 + - - -
89F HIS* 1.3 72.8 - - - +
91F GLU* 1.3 69.2 + - - +
143F SER* 3.0 11.8 + - - -
144F LEU* 4.6 0.4 - - - +
145F PHE* 5.4 7.6 - - - -
245F ARG* 3.7 3.5 - - - +
246F PHE* 2.9 33.0 + - - +
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Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F HIS* 2.7 25.5 + - - -
90F GLY* 1.3 83.7 - - - +
92F GLN* 1.3 58.2 + - - +
143F SER* 3.3 36.9 + - - +
161F VAL* 5.1 7.3 - - - +
162F LYS 4.6 1.2 - - - +
163F VAL* 5.7 0.2 - - - -
164F ALA* 3.9 4.4 + - - +
243F LYS* 3.0 28.6 + - - +
244F ALA 3.3 9.0 - - - +
245F ARG* 2.7 48.7 + - + -
246F PHE* 4.1 3.1 - - - -
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Residues in contact with GLN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F VAL* 4.0 13.0 - - + +
89F HIS* 2.8 29.8 + - - +
91F GLU* 1.3 75.5 - - - +
93F TYR* 1.3 74.9 + - - +
140F ASN* 3.1 29.3 + - - +
141F GLN 3.9 5.4 - - - +
142F PHE* 3.2 21.8 - - - -
217F LEU* 3.8 14.4 - - + -
220F PHE* 4.1 21.2 - - + -
242F VAL 4.6 0.2 - - - -
243F LYS* 3.2 8.1 - - - +
244F ALA* 3.0 31.7 + - - +
246F PHE* 4.0 15.5 - - + -
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Residues in contact with TYR 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F GLN* 1.3 85.6 + - - +
94F LEU* 1.3 61.3 + - - +
95F GLU* 2.9 46.3 + - + +
139F HIS* 3.8 13.0 - - - -
140F ASN* 3.2 5.4 - - - -
141F GLN* 2.8 48.1 + - + +
162F LYS* 3.4 56.8 + - + -
241F ALA* 4.0 13.4 - - + +
242F VAL 3.3 17.3 - - - -
243F LYS* 4.0 15.5 - - + +
285F TYR* 4.0 15.9 - - - -
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F PRO 3.4 27.4 - - - +
59F THR* 3.8 17.5 - - + -
61F GLY* 4.0 3.8 - - - -
62F VAL* 3.9 20.0 - - + +
92F GLN* 4.9 0.2 - - - +
93F TYR* 1.3 78.0 - - - +
95F GLU* 1.3 71.4 + - - +
96F LEU* 4.1 11.2 - - + -
138F CYS* 4.0 13.9 - - + -
139F HIS 3.2 15.3 - - - +
140F ASN* 3.5 24.0 - - - +
220F PHE* 5.2 0.7 - - + -
239F PHE* 5.7 3.0 - - + -
241F ALA* 3.1 5.2 - - - +
242F VAL* 2.9 43.6 + - + +
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Residues in contact with GLU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F TYR* 2.9 33.0 + - + +
94F LEU* 1.3 74.3 - - - +
96F LEU* 1.3 67.8 + - - +
97F TYR* 3.5 43.6 + - + -
138F CYS* 3.2 5.7 - - - +
139F HIS* 2.8 36.2 + - + +
162F LYS* 4.4 7.1 + - - -
240F LYS* 3.5 12.6 - - + +
241F ALA* 3.9 5.4 - - + -
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F PRO* 3.5 46.0 - - + +
61F GLY* 5.1 0.2 - - - -
94F LEU* 4.1 11.7 - - + -
95F GLU* 1.3 75.6 - - - +
97F TYR* 1.3 65.5 + - - +
98F LYS* 3.3 11.8 + - - +
99F PRO* 5.4 2.2 - - + -
100F LEU* 4.0 24.7 - - + +
137F ILE 3.7 2.2 - - - -
138F CYS* 3.6 24.2 - - + -
236F VAL* 5.6 1.6 - - + +
239F PHE* 3.6 24.8 - - + +
240F LYS* 2.8 23.5 + - - +
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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