Contacts of the strand formed by residues 87 - 92 (chain C) in PDB entry 3QEM
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 VAL 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C ASN* 3.2 22.0 - - + +
29C ILE 4.6 0.2 - - - +
30C GLY* 3.7 21.3 - - - -
63C THR* 4.8 6.1 - - - +
82C LEU* 3.1 37.7 - - + +
83C ILE* 3.9 11.2 - - + +
85C SER 4.5 0.4 - - - +
86C GLN* 1.3 74.3 - - - +
88C TYR* 1.3 64.1 + - - +
89C ALA 3.9 8.3 - - - +
90C ILE* 4.3 13.9 - - + -
116C ILE* 3.3 29.0 - - + +
325C PRO* 3.7 8.3 - - - +
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Residues in contact with TYR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE 5.5 0.4 - - - -
27C VAL* 3.7 32.4 - - + +
28C ASN 3.0 11.8 + - - +
29C ILE* 5.5 0.2 - - - -
86C GLN* 4.0 11.4 - - + -
87C VAL* 1.3 73.8 - - - +
89C ALA* 1.3 62.9 + - + +
116C ILE* 3.6 3.2 - - - +
117C PRO* 3.4 14.0 - - - +
313C ILE* 3.8 28.9 - - + -
316C LEU* 4.7 11.4 - - + -
317C PHE* 3.8 27.0 - + - -
322C ILE* 5.0 1.8 + - + +
323C THR 4.1 4.8 + - - -
324C ASP* 2.6 29.5 + - - -
325C PRO* 3.4 20.9 - - + +
336C TRP* 3.5 33.9 - + - -
342C PHE* 3.2 16.8 - + + -
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASN 4.2 1.2 + - - -
29C ILE* 4.8 2.3 - - - +
30C GLY* 2.6 34.4 + - - +
87C VAL* 3.2 4.0 - - - +
88C TYR* 1.3 82.2 - - - +
90C ILE* 1.3 63.0 + - - +
91C LEU* 4.9 3.1 - - + -
116C ILE* 3.8 2.9 - - - -
117C PRO* 3.4 16.4 - - + +
119C ILE* 5.1 4.3 - - + -
309C VAL* 4.4 26.5 - - + -
342C PHE* 4.1 13.5 - - + -
346C LEU* 5.4 0.2 - - + -
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Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY* 2.8 8.7 - - - +
31C ALA* 4.1 2.9 - - - -
32C VAL* 4.4 1.3 - - + +
78C VAL* 4.0 19.3 - - + -
82C LEU* 3.8 36.1 - - + -
83C ILE* 5.1 1.3 - - + -
87C VAL* 4.3 15.9 - - + -
89C ALA* 1.3 82.5 - - - +
91C LEU* 1.3 78.1 + - - +
92C VAL* 4.2 0.7 - - + -
107C ILE* 4.1 17.7 - - + -
111C ALA* 4.1 19.3 - - + -
116C ILE* 4.8 5.2 - - + -
117C PRO 3.2 5.5 + - - -
118C VAL* 3.4 12.1 - - + +
119C ILE* 2.9 24.4 + - - -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 5.2 4.7 - - + -
30C GLY 2.7 22.0 + - - +
31C ALA* 3.4 8.4 - - + -
32C VAL 2.8 27.9 + - - +
33C LEU* 5.1 0.9 - - + -
42C PHE* 4.2 15.0 - - + -
89C ALA* 4.9 2.7 - - + +
90C ILE* 1.3 82.2 - - - +
92C VAL* 1.3 63.6 + - - +
119C ILE* 3.3 13.9 - - + +
121C LEU* 4.0 18.2 - - + -
302C ILE* 4.6 3.8 - - + +
305C ALA* 3.6 31.4 - - + -
306C VAL* 3.8 24.0 - - + +
309C VAL* 4.7 17.3 - - + -
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 3.5 7.2 - - + +
67C HIS* 4.7 4.7 - - - +
90C ILE* 4.2 2.7 - - + -
91C LEU* 1.3 80.1 - - - +
93C SER* 1.3 65.0 + - - +
94C HIS 4.5 0.2 - - - +
104C PRO* 3.4 38.4 - - + -
107C ILE* 3.4 45.8 - - + -
118C VAL* 4.0 14.4 - - + -
119C ILE 2.8 10.4 + - - +
120C GLY* 3.4 5.2 - - - -
121C LEU* 2.7 35.4 + - - +
122C THR 4.3 0.2 + - - -
123C THR* 5.6 0.3 + - - +
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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