Contacts of the strand formed by residues 93 - 102 (chain H) in PDB entry 3WBR
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 93 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83H CYS* 3.9 2.3 - - - -
89H SER* 3.5 5.0 - - - -
90H PHE 2.9 29.5 + - - -
91H GLN* 3.4 1.3 + - - +
92H SER* 1.3 85.1 + - - +
94H CYS* 1.3 65.0 + - - +
95H TYR* 3.7 26.4 + - - -
207H LYS* 4.0 21.2 + - - +
208H MET 3.3 10.1 + - - -
209H LYS* 4.2 4.4 - - - +
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Residues in contact with CYS 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H CYS* 2.0 52.3 - - + -
84H PRO* 4.9 0.4 - - - -
87H TRP* 3.5 18.7 - - + -
88H THR 3.4 4.0 - - - -
93H SER* 1.3 73.2 - - - +
95H TYR* 1.3 63.0 + - - +
207H LYS* 3.3 7.1 - - - +
208H MET* 2.6 47.4 + - + +
209H LYS 4.2 14.1 - - - -
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Residues in contact with TYR 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H PRO 4.6 0.3 - - - +
87H TRP* 3.2 11.9 - - - -
88H THR* 2.7 45.1 + - - +
90H PHE* 3.5 29.2 + - + -
91H GLN* 5.5 0.3 + - - -
93H SER* 3.7 23.9 + - - -
94H CYS* 1.3 76.4 - - - +
96H PHE* 1.3 59.0 + - - +
97H ILE* 5.3 4.9 - - + -
119H VAL* 4.1 12.3 - - + -
126H GLU* 2.6 33.6 + - + +
129H PHE* 3.5 22.9 - + + -
130H ILE* 4.1 22.0 - - + -
133H ASN* 5.5 2.9 - - + +
205H ILE* 4.8 5.6 - - + -
206H CYS 3.4 7.9 - - - -
207H LYS* 3.5 28.5 - - + +
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Residues in contact with PHE 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H PRO* 3.9 30.5 - - + -
87H TRP* 3.6 42.4 - + + +
95H TYR* 1.3 74.7 - - - +
97H ILE* 1.3 79.6 + - - +
98H SER* 3.4 28.4 + - - -
110H ASN* 5.2 0.2 - - - -
114H MET* 4.3 26.0 - - + -
205H ILE* 3.4 5.0 - - - +
206H CYS* 2.8 43.4 + - + +
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Residues in contact with ILE 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H TYR* 5.3 4.3 - - + -
96H PHE* 1.3 97.4 - - - +
98H SER* 1.3 64.1 + - - +
99H THR* 3.7 15.5 + - + +
130H ILE* 5.5 1.1 - - + +
133H ASN* 3.7 31.6 - - + +
134H LEU* 3.7 20.9 - - + -
140H TYR* 3.4 35.9 - - + +
204H SER 3.7 2.2 - - - +
205H ILE* 3.8 17.9 - - + -
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Residues in contact with SER 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H PHE* 3.4 23.6 + - - -
97H ILE* 1.3 74.5 - - - +
99H THR* 1.3 60.3 + - - +
100H GLY* 3.3 6.2 + - - -
102H GLN* 6.1 0.4 - - - -
110H ASN* 3.5 20.1 + - - -
203H LYS* 3.3 7.8 - - - +
204H SER* 2.9 47.9 + - - +
206H CYS* 3.9 9.4 - - - -
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Residues in contact with THR 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASN* 4.7 8.9 + - - +
203E LYS* 4.6 5.7 + - - -
97H ILE* 3.7 18.1 + - + +
98H SER* 1.3 73.7 - - - +
100H GLY* 1.3 63.0 + - - +
101H MET* 3.9 1.0 + - - +
135H LYS* 5.4 7.6 - - + +
140H TYR* 5.9 0.9 - - + -
203H LYS* 3.2 35.5 - - + +
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Residues in contact with GLY 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASN* 3.9 22.8 - - - +
98H SER* 3.3 8.1 - - - +
99H THR* 1.3 83.5 + - - +
101H MET* 1.3 59.2 + - - -
102H GLN* 3.9 9.7 + - - +
202H GLN 3.4 1.9 - - - +
203H LYS* 3.2 20.4 - - - -
204H SER* 4.5 1.0 + - - -
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Residues in contact with MET 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E MET* 3.7 18.4 - - + +
137E ASN* 2.7 24.5 + - - +
138E SER* 3.9 9.9 - - - -
139E SER* 3.4 36.3 - - - +
202E GLN* 3.4 30.5 - - - +
203E LYS* 4.1 22.7 - - - +
99H THR 4.7 0.9 - - - +
100H GLY* 1.3 72.4 - - - +
102H GLN* 1.3 66.4 + - - +
201H PRO* 3.4 24.7 - - + +
202H GLN 3.4 7.6 - - - -
203H LYS* 4.1 17.9 - - + +
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Residues in contact with GLN 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASN* 6.5 0.7 - - + -
100H GLY* 3.9 6.7 + - - +
101H MET* 1.3 83.2 - - - +
103H SER* 1.3 65.5 + - - +
106H LYS* 3.6 38.1 - - + +
107H SER* 3.5 10.8 + - - +
110H ASN* 3.8 18.6 - - - +
141H PHE* 3.3 3.3 - - - -
201H PRO* 3.6 8.5 - - - -
202H GLN 2.9 28.8 + - - +
204H SER* 5.5 0.7 + - - -
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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