Contacts of the strand formed by residues 88 - 96 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H VAL* 1.3 83.2 - - - +
89H HIS* 1.3 65.2 + - - +
144H LEU* 3.3 4.9 - - - -
145H PHE* 2.6 59.9 + - + +
146H LEU* 6.1 0.4 - - - -
197H LEU* 4.8 18.8 - - + -
207H ALA* 6.3 2.5 - - + -
209H PHE* 5.2 16.8 - - + -
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Residues in contact with HIS 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H VAL 4.2 0.6 + - - -
88H LEU* 1.3 76.4 - - - +
90H GLY* 1.3 61.4 + - - +
91H GLU 2.9 29.4 + - - -
92H GLN* 3.0 21.4 + - - -
142H PHE* 4.0 13.8 - + - -
143H SER 3.5 8.6 + - - -
144H LEU* 4.5 8.5 - - + +
145H PHE* 5.5 0.4 - - - -
216H GLY* 6.0 4.0 - - - +
217H LEU* 3.6 38.5 + - + +
246H PHE* 3.7 25.0 - + + +
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Residues in contact with GLY 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H LEU 3.6 2.8 + - - -
89H HIS* 1.3 74.8 - - - +
91H GLU* 1.3 65.7 + - - +
143H SER* 2.7 19.9 + - - -
144H LEU* 4.6 0.2 - - - +
145H PHE* 4.7 8.2 - - - +
245H ARG* 4.1 0.9 - - - +
246H PHE* 2.8 35.7 + - - +
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Residues in contact with GLU 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H HIS* 2.9 19.4 + - - -
90H GLY* 1.3 82.6 - - - +
92H GLN* 1.3 62.0 + - - +
141H GLN 4.5 0.2 - - - -
143H SER* 3.1 34.9 + - - +
161H VAL* 4.8 9.4 - - - +
164H ALA* 4.2 1.8 + - - +
243H LYS* 3.1 27.9 + - - +
244H ALA 3.3 11.4 - - - +
245H ARG* 2.7 49.3 + - + +
246H PHE* 3.8 6.1 - - - -
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Residues in contact with GLN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62H VAL* 3.7 11.4 - - - +
89H HIS* 3.0 19.4 + - - -
91H GLU* 1.3 75.6 - - - +
93H TYR* 1.3 76.5 + - - +
140H ASN* 3.2 31.1 + - - +
141H GLN 3.6 6.5 - - - +
142H PHE* 3.3 20.4 - - - -
217H LEU* 3.5 21.5 - - + -
220H PHE* 4.0 23.4 - - + -
242H VAL 4.1 0.3 - - - +
243H LYS* 3.5 4.7 - - - +
244H ALA* 3.1 30.0 + - - +
246H PHE* 3.9 18.6 - - + -
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Residues in contact with TYR 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H GLN* 1.3 83.8 + - - +
94H LEU* 1.3 65.0 + - - +
95H GLU* 2.8 45.8 + - + +
139H HIS* 3.9 21.8 - + - -
140H ASN* 3.2 5.5 - - - -
141H GLN* 2.8 43.5 + - + +
162H LYS* 3.5 50.1 + - + -
241H ALA* 3.9 9.8 - - + +
242H VAL 3.4 16.8 - - - -
243H LYS* 3.9 20.2 - - + +
285H TYR* 3.9 16.8 - - - -
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Residues in contact with LEU 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H PRO 3.5 25.6 - - - +
59H THR* 3.6 19.5 - - + -
61H GLY* 4.1 4.9 - - - -
62H VAL* 3.7 21.5 - - + +
93H TYR* 1.3 78.1 - - - +
95H GLU* 1.3 73.7 + - - +
96H LEU* 4.1 12.8 - - + -
138H CYS* 4.1 11.9 - - + -
139H HIS 3.3 8.7 - - - +
140H ASN* 3.5 26.7 - - - +
220H PHE* 5.1 0.4 - - + -
239H PHE* 5.7 0.9 - - + -
241H ALA* 3.2 4.0 - - - +
242H VAL* 2.9 45.4 + - + +
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Residues in contact with GLU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H TYR* 2.8 35.5 + - + +
94H LEU* 1.3 75.6 - - - +
96H LEU* 1.3 67.1 + - - +
97H TYR* 3.4 43.9 + - + -
138H CYS* 3.2 7.4 - - - +
139H HIS* 3.0 32.8 + - + +
162H LYS* 4.3 9.5 + - - -
240H LYS* 3.4 12.1 - - + +
241H ALA* 3.7 5.8 - - + -
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Residues in contact with LEU 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H PRO* 3.5 47.6 - - + +
94H LEU* 4.1 13.7 - - + +
95H GLU* 1.3 75.7 - - - +
97H TYR* 1.3 66.3 + - - +
98H LYS* 3.1 12.7 + - - +
99H PRO* 5.2 2.2 - - + -
100H LEU* 4.0 23.3 - - + +
137H ILE 3.7 2.5 - - - -
138H CYS* 3.9 20.9 - - + -
236H VAL* 5.4 1.8 - - + +
239H PHE* 3.4 28.4 - - + +
240H LYS* 2.7 25.8 + - - +
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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