Contacts of the strand formed by residues 95 - 99 (chain C) in PDB entry 2Q41
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 95 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 6.2 0.2 - - - -
50C GLU* 3.5 12.3 - - - +
51C MSE 5.1 0.2 - - - +
52C SER* 4.9 8.7 - - - +
55C TRP* 3.7 20.2 - - + -
91C VAL* 3.0 4.6 - - - +
92C LEU 2.8 25.0 + - - +
93C ASP* 3.6 13.7 - - + +
94C GLY* 1.3 77.6 - - - +
96C ILE* 1.3 67.0 + - - +
97C GLN* 2.7 35.7 + - - +
203C SER* 6.4 0.4 - - - -
204C ASP* 3.6 29.8 - - + +
206C ILE* 5.8 4.9 - - + -
271C PRO* 5.6 2.2 - - + -
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 4.1 11.9 - - + -
50C GLU* 2.7 55.7 + - + +
60C HIS* 4.1 12.3 - - + -
62C LEU* 4.4 18.4 - - + -
89C VAL* 4.0 20.0 - - + -
90C LEU 3.8 4.5 - - - -
91C VAL* 3.9 5.9 - - + +
94C GLY 4.2 0.2 - - - -
95C VAL* 1.3 75.6 - - - +
97C GLN* 1.3 65.1 + - - +
98C LEU 4.1 10.3 - - - +
99C THR* 4.4 1.8 - - - +
269C THR* 3.7 33.7 - - + +
270C TYR* 3.5 15.5 - - + -
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Residues in contact with GLN 97 (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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90C LEU* 2.8 17.8 + - + +
91C VAL 4.2 0.2 - - - -
92C LEU* 3.4 45.6 + - + +
95C VAL* 2.7 44.0 + - - +
96C ILE* 1.3 75.2 + - - +
98C LEU* 1.3 76.9 + - + +
106C TYR* 5.6 0.5 - - - -
130C GLY* 5.8 2.7 - - - +
202C SER 4.8 3.3 - - - +
203C SER* 3.8 26.4 + - - +
204C ASP* 5.3 0.6 + - - -
270C TYR* 2.7 29.9 + - - -
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Residues in contact with LEU 98 (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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89C VAL* 3.5 7.8 - - - +
90C LEU* 3.2 54.2 + - + -
96C ILE* 3.7 4.3 - - - +
97C GLN* 1.3 86.3 - - + +
99C THR* 1.3 67.1 + - - +
103C GLU* 4.0 20.6 - - + +
107C GLN* 4.9 2.7 - - + +
130C GLY* 4.1 5.8 - - - +
131C ASP* 3.0 47.6 - - + +
164C PHE* 4.2 21.1 - - + -
269C THR* 4.9 2.0 - - - -
270C TYR* 5.0 3.1 - - - -
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Residues in contact with THR 99 (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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62C LEU* 4.9 0.2 - - - +
86C TYR* 3.2 43.4 - - + +
88C LYS 3.5 6.3 - - - +
89C VAL* 4.1 11.7 - - + +
96C ILE* 4.4 2.3 - - - +
98C LEU* 1.3 78.2 + - - +
100C GLU* 1.3 55.5 + - - +
101C ARG* 3.1 18.4 - - + +
102C ASP* 2.9 18.5 + - - +
103C GLU* 2.7 37.3 + - - +
269C THR* 3.1 21.7 + - - +
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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