Contacts of the strand formed by residues 109 - 118 (chain C) in PDB entry 3BZE
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 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C CYS* 6.2 0.2 - - + -
102C GLU 4.3 2.9 - - - -
108C ARG* 1.3 78.4 + - - +
110C LEU* 1.3 64.5 + - - +
111C ARG* 3.9 31.9 - - + +
112C GLY* 3.9 7.2 - - - -
130C LEU* 4.7 14.8 - - + -
160C LEU* 5.1 3.8 - - + -
161C GLU* 3.2 54.3 - - + +
165C VAL* 4.4 18.5 - - + +
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Residues in contact with LEU 110 (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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2C SER* 4.6 8.3 - - - +
102C GLU* 3.1 30.9 + - + +
103C LEU 3.8 5.6 - - - +
104C GLY* 3.2 37.0 - - - +
105C PRO* 4.1 11.0 - - + -
106C ASP* 5.9 0.9 - - - +
108C ARG 2.3 9.9 + - - -
109C PHE* 1.3 78.6 - - - +
111C ARG* 1.3 68.6 + - + +
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Residues in contact with ARG 111 (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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3B ARG* 5.3 11.5 - - - +
101C CYS* 3.7 3.5 - - - +
102C GLU* 3.1 42.5 + - + +
109C PHE* 3.2 23.4 - - + -
110C LEU* 1.3 90.8 + - + +
112C GLY* 1.3 98.1 + - - +
113C TYR* 3.2 31.7 - - - +
128C GLU* 4.0 32.1 + - - +
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Residues in contact with GLY 112 (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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100C GLY 3.1 14.8 - - - -
101C CYS* 4.5 0.9 - - - -
109C PHE* 3.9 12.1 - - - -
111C ARG* 1.3 101.5 + - - +
113C TYR* 1.3 63.9 + - - -
128C GLU* 5.5 0.5 - - - +
130C LEU* 5.4 9.3 - - - +
160C LEU* 5.1 8.1 - - - -
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Residues in contact with TYR 113 (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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6C LYS* 2.3 50.1 - - + +
8C PHE* 5.3 0.2 - + - -
98C MET* 4.4 18.8 - - + -
99C HIS* 3.6 15.3 - - - -
100C GLY* 3.3 30.9 + - - -
101C CYS 4.6 0.7 - - - -
102C GLU* 4.1 22.8 + - + -
111C ARG* 3.2 31.9 - - - +
112C GLY* 1.3 75.6 - - - -
114C GLU* 1.3 85.5 + - - +
115C GLN* 5.2 7.6 - - - +
126C LEU* 5.6 2.5 - - - -
130C LEU* 5.8 4.5 - - - -
160C LEU* 3.7 12.4 - - - +
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Residues in contact with GLU 114 (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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97C TRP* 3.4 30.8 + - - +
98C MET 2.9 13.9 - - - +
99C HIS* 3.6 10.1 - - + +
113C TYR* 1.3 85.6 - - - +
115C GLN* 1.3 74.9 + - - +
116C PHE* 4.4 1.1 - - + -
125C THR* 3.9 4.7 - - - +
126C LEU* 3.9 25.5 + - + +
133C TRP* 3.4 17.9 - - + -
156C GLN* 2.6 46.8 - - - +
160C LEU* 3.1 19.9 - - + +
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Residues in contact with GLN 115 (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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97C TRP* 3.3 2.8 - - - -
98C MET* 2.9 40.6 + - + +
113C TYR* 5.2 8.2 - - + +
114C GLU* 1.3 83.9 - - - +
116C PHE* 1.3 68.6 + - - +
122C ASP* 3.7 18.4 + - - -
124C LEU 3.3 12.8 - - - +
125C THR* 3.1 28.9 + - - +
126C LEU 4.7 0.9 - - - +
58D LYS 5.5 1.3 - - - +
60D TRP* 3.4 27.9 - - + -
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Residues in contact with PHE 116 (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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74C PHE* 3.9 15.5 - + - -
95C LEU* 4.3 17.3 - - + -
96C GLN 3.2 7.2 - - - +
97C TRP* 3.3 48.7 - + + -
114C GLU* 4.4 1.1 - - - -
115C GLN* 1.3 79.3 + - - +
117C ALA* 1.3 62.1 + - - +
122C ASP* 3.9 0.5 - - - -
123C TYR* 2.9 26.8 + - + -
124C LEU* 2.6 36.8 + - + +
125C THR* 5.2 0.2 + - - -
133C TRP* 3.7 29.2 - + - -
60D TRP* 3.8 7.3 - - - -
6Q THR* 3.9 11.2 - - - -
7Q LEU* 4.1 21.5 - - + -
9Q LEU* 4.6 13.0 - - + -
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Residues in contact with ALA 117 (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 LEU* 3.4 9.8 - - - +
96C GLN* 2.8 39.1 + - + +
116C PHE* 1.3 75.1 - - - +
118C TYR* 1.3 60.8 + - - +
119C ASP 4.2 0.4 - - - -
120C GLY 4.9 0.4 - - - -
121C LYS 3.2 19.5 - - - +
123C TYR* 3.9 3.4 - - - -
60D TRP* 3.4 42.6 - - + -
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Residues in contact with TYR 118 (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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78C LEU* 4.1 10.7 + - + -
81C LEU* 3.4 43.3 - - + +
82C ARG* 4.3 3.1 + - - +
85C TYR* 3.6 51.4 - + - +
87C GLN* 2.9 11.1 + - - -
93C HIS* 2.8 36.4 + - + +
94C THR 3.2 12.8 - - - -
95C LEU* 4.7 0.7 - - - -
117C ALA* 1.3 73.0 - - - +
119C ASP* 1.3 89.3 + - + +
120C GLY 3.2 0.4 - - - -
121C LYS* 3.0 23.9 + - - +
123C TYR* 3.9 21.2 - - + +
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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