Contacts of the strand formed by residues 93 - 100 (chain C) in PDB entry 2Q2U
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 PHE 93 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 5.8 0.2 - - + -
52C MET* 3.5 52.9 - - + -
55C LEU* 4.3 10.1 - - + -
56C LEU* 4.3 15.7 - - + -
68C ILE* 4.1 4.7 - - + -
69C SER 4.2 2.0 - - - +
70C ILE* 3.3 27.6 - - + +
71C GLU* 5.2 1.6 - - - +
89C TYR* 4.1 4.7 - + + -
91C ALA 3.9 8.7 - - - -
92C LYS* 1.3 82.8 - - - +
94C SER* 1.3 73.8 + - - +
95C TYR* 5.4 0.4 - - + -
131C GLN* 3.5 10.8 + - + +
132C VAL* 3.2 49.4 - - + -
133C LYS* 3.0 21.2 + - - +
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Residues in contact with SER 94 (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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67C GLU 4.5 0.2 - - - -
68C ILE* 3.6 4.2 - - - -
69C SER 3.0 36.5 + - - -
71C GLU* 3.1 37.6 + - - +
93C PHE* 1.3 83.7 + - - +
95C TYR* 1.3 61.3 + - - +
96C TYR* 4.3 3.8 - - - -
132C VAL* 5.2 0.2 - - - -
133C LYS* 3.2 23.5 - - - +
135C ILE* 3.7 12.0 - - - +
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER 2.8 27.9 + - - -
39C MET* 3.9 12.9 - - + +
56C LEU* 3.8 25.1 - - + -
60C LEU* 3.4 36.0 - - + +
64C SER 3.5 9.5 + - - -
65C ASP 3.3 3.8 - - - -
66C GLY* 2.9 26.3 + - - -
67C GLU 3.3 10.8 - - - -
68C ILE* 3.8 20.9 - - + -
93C PHE* 5.4 0.7 - - + -
94C SER* 1.3 75.4 - - - +
96C TYR* 1.3 60.0 + - - +
97C TRP* 3.2 24.7 + + + -
132C VAL* 4.8 2.9 - - + -
133C LYS 3.0 9.1 + - - +
134C ILE* 3.6 7.6 - - + +
135C ILE* 2.9 24.0 + - - -
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Residues in contact with TYR 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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28C ILE* 3.4 37.2 - - + -
66C GLY* 2.9 24.8 - - - -
67C GLU* 2.8 22.4 + - + +
69C SER* 4.3 15.9 - - - -
71C GLU* 2.6 34.2 + - - -
94C SER* 4.4 2.2 - - - -
95C TYR* 1.3 75.7 - - - +
97C TRP* 1.3 60.9 + - - +
98C PHE* 3.4 4.9 + - + -
135C ILE* 3.2 36.7 - - + +
137C LEU* 3.6 36.6 - - + -
160C PHE* 4.3 20.3 - + - -
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Residues in contact with TRP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 4.1 8.7 - - + -
61C PRO* 3.7 24.7 - - + -
64C SER* 3.0 34.0 + - - +
65C ASP 3.3 10.8 - - - -
95C TYR* 3.2 16.4 + + + -
96C TYR* 1.3 68.5 - - - +
98C PHE* 1.3 59.0 + - - +
99C ASP 2.8 28.5 + - - -
100C TYR* 3.8 12.3 - + - -
116C MET* 3.2 43.3 - - + +
119C TYR* 3.8 13.9 - + + -
120C ILE* 4.1 24.2 - - + -
126C ILE* 4.2 12.1 - - + -
134C ILE* 4.3 20.0 - - + -
135C ILE 2.8 11.6 + - - +
136C PRO* 4.3 4.0 - - + -
137C LEU 2.8 26.1 + - - -
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Residues in contact with PHE 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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25C THR* 5.4 4.3 - - - +
28C ILE* 5.7 2.2 - - + -
32C ARG* 3.5 27.4 - - - -
65C ASP* 3.0 30.7 + - - -
66C GLY* 3.3 21.5 - - - -
67C GLU* 3.9 13.9 - - + -
96C TYR* 3.6 15.3 - - + -
97C TRP* 1.3 74.4 - - - +
99C ASP* 1.3 64.6 + - + +
109C TYR* 3.8 25.4 + - - +
113C VAL* 5.3 2.3 - - - +
116C MET* 4.2 7.0 - - - +
137C LEU* 3.9 34.2 - - + +
166C ARG* 3.5 23.0 + - - +
184C LEU* 6.4 0.4 - - + -
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Residues in contact with ASP 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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7C LEU* 4.1 1.6 - - - +
65C ASP* 3.1 34.3 + - + +
97C TRP* 2.8 22.4 + - - -
98C PHE* 1.3 83.9 - - + +
100C TYR* 1.3 69.8 + - - +
109C TYR* 4.6 2.7 - - - -
112C ARG* 2.8 36.2 + - - +
113C VAL* 6.4 1.1 - - - +
116C MET* 4.1 4.0 - - - -
166C ARG* 2.8 30.1 + - - -
172C TYR* 3.2 20.9 - - + -
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Residues in contact with TYR 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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61C PRO* 3.4 31.5 - - + +
62C GLU 3.5 22.0 + - - -
63C GLY 3.2 16.6 - - - -
64C SER* 4.2 0.2 - - - -
97C TRP* 3.8 12.8 - + - +
99C ASP* 1.3 84.4 + - - +
101C VAL* 1.3 63.9 + - - +
102C THR* 3.3 34.4 + - + +
112C ARG* 3.6 35.9 + - - +
115C ASP* 3.8 15.6 - - + +
116C MET* 3.8 31.2 - - + -
119C TYR* 3.9 19.0 - + + -
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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