Contacts of the helix formed by residues 94 - 104 (chain C) in PDB entry 2QY7
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 SER 94 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C THR* 2.8 42.6 + - - -
52C PHE* 3.5 21.7 - - - -
93C GLY* 1.3 76.2 - - - +
95C GLU* 1.3 63.0 + - - +
96C ARG* 2.8 32.8 + - - +
97C VAL* 3.0 20.1 + - - +
98C VAL 4.0 0.5 + - - -
149C ARG* 3.5 4.2 + - - -
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Residues in contact with GLU 95 (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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52C PHE* 5.0 1.4 - - - -
94C SER* 1.3 74.5 + - - +
96C ARG* 1.3 63.4 + - + +
98C VAL* 3.0 45.4 + - - +
99C THR* 3.3 10.7 + - - +
102C ARG* 5.1 2.4 + - - -
149C ARG* 3.1 33.3 + - - +
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Residues in contact with ARG 96 (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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51C THR 5.1 1.9 + - - -
54C TYR* 3.3 43.1 + - - +
57C PHE* 3.3 53.4 - - + +
58C PRO* 4.2 12.9 - - - +
94C SER* 2.8 17.2 + - - +
95C GLU* 1.3 80.3 - - + +
97C VAL* 1.3 55.1 + - - +
99C THR* 3.4 9.4 + - - -
100C SER* 3.0 23.4 + - - -
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C THR* 3.8 26.9 - - + -
57C PHE* 3.8 19.7 - - + -
61C MET* 4.5 9.8 - - + +
86C LEU* 4.0 10.5 - - + -
89C LEU* 3.7 38.1 - - + +
90C ILE* 3.7 15.0 - - + +
94C SER 3.0 19.0 + - - +
96C ARG* 1.3 74.0 - - - +
98C VAL* 1.3 60.0 + - - +
100C SER* 3.4 4.1 + - - -
101C ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 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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90C ILE* 4.0 10.3 - - + +
95C GLU* 3.0 29.5 + - - +
97C VAL* 1.3 76.6 - - - +
99C THR* 1.3 62.0 + - - +
101C ALA* 3.4 5.4 + - - +
102C ARG* 3.0 58.8 + - + +
139C ALA* 6.3 0.4 - - + -
145C LEU* 3.5 22.4 - - + -
149C ARG* 3.6 34.3 - - - +
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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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95C GLU* 3.3 13.2 + - - +
96C ARG* 3.7 12.2 - - - -
97C VAL 3.3 0.2 - - - -
98C VAL* 1.3 77.3 - - - +
100C SER* 1.3 57.7 + - - +
102C ARG* 3.3 11.0 + - - +
103C GLU* 2.8 56.2 + - + +
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Residues in contact with SER 100 (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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57C PHE* 4.3 10.3 - - - -
61C MET* 3.4 17.1 - - - +
65C TRP* 3.0 25.6 + - - -
96C ARG 3.0 17.1 + - - -
97C VAL 3.6 4.5 - - - -
98C VAL 3.3 0.2 - - - -
99C THR* 1.3 73.8 - - - +
101C ALA* 1.3 65.7 + - - +
103C GLU* 3.2 3.7 + - - +
104C HIS* 2.8 38.5 + - - -
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Residues in contact with ALA 101 (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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61C MET* 5.2 0.2 - - - +
65C TRP* 3.8 15.1 - - + -
86C LEU* 4.5 8.5 - - + -
90C ILE* 3.6 30.1 - - + -
97C VAL 2.9 17.4 + - - +
98C VAL* 3.8 4.7 - - - +
100C SER* 1.3 74.3 - - - +
102C ARG* 1.3 57.7 + - - +
104C HIS 3.3 3.1 + - - -
105C ILE* 3.0 32.2 + - - +
108C LEU* 4.3 4.9 - - + +
139C ALA* 4.7 8.5 - - + -
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Residues in contact with ARG 102 (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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95C GLU* 5.1 3.0 + - - -
98C VAL* 3.0 46.3 + - + +
99C THR* 3.7 11.3 + - - +
101C ALA* 1.3 75.0 - - - +
103C GLU* 1.3 64.5 + - + +
105C ILE* 3.2 29.6 + - + +
139C ALA* 3.7 28.8 + - + +
140C GLN* 5.9 0.9 - - + +
142C ASP* 2.6 42.8 + - - -
145C LEU* 4.0 4.0 - - - +
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C THR* 2.8 43.0 + - + +
100C SER* 3.2 5.4 + - - +
102C ARG* 1.3 77.7 - - + +
104C HIS* 1.3 68.4 + - + +
105C ILE 3.5 0.4 - - - -
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Residues in contact with HIS 104 (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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65C TRP* 3.6 50.4 + + + +
69C LEU* 5.8 0.4 - - - +
100C SER* 2.8 33.7 + - - +
101C ALA 3.3 2.7 - - - -
103C GLU* 1.3 87.7 + - + +
105C ILE* 1.3 62.8 + - - +
106C TYR 3.2 3.6 - - - -
107C ASP* 3.0 37.8 + - + +
108C LEU* 3.1 13.5 + - - +
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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