Contacts of the strand formed by residues 93 - 102 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C CYS* 3.6 2.0 - - - -
90C PHE 2.9 33.7 + - - -
91C GLN 3.3 0.8 + - - -
92C SER* 1.3 82.0 + - - +
94C CYS* 1.3 65.0 + - - +
95C TYR* 3.7 23.3 - - - -
207C LYS* 3.6 20.3 + - - -
208C MET 3.4 11.2 + - - -
209C LYS* 4.4 6.4 - - - +
210C LYS* 3.4 7.6 + - - +
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Residues in contact with CYS 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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83C CYS* 2.0 50.3 - - + -
84C PRO* 4.0 5.4 - - - -
87C TRP* 3.4 19.2 - - + -
88C THR 3.3 4.5 - - - -
93C SER* 1.3 72.3 - - - +
95C TYR* 1.3 62.2 + - - +
207C LYS* 3.2 6.9 - - - +
208C MET* 2.7 42.4 + - + +
209C LYS 4.7 1.1 - - - -
210C LYS* 3.2 28.0 - - - -
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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
----------------------------------------------------------
86C PRO 4.7 0.5 - - - +
87C TRP* 3.3 10.9 - - - -
88C THR* 2.9 42.9 + - - +
90C PHE* 3.8 26.2 + - + -
93C SER* 3.7 30.5 - - - -
94C CYS* 1.3 75.8 - - - +
96C PHE* 1.3 58.6 + - - +
97C ILE* 5.4 4.5 - - + -
119C VAL* 3.9 14.1 - - + -
126C GLU* 2.4 37.0 + - + +
129C PHE* 3.5 24.5 - + + -
130C ILE* 4.1 17.7 - - + -
205C ILE* 4.7 7.4 - - + -
206C CYS 3.3 7.2 - - - +
207C LYS* 3.6 22.4 - - + -
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Residues in contact with PHE 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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86C PRO* 4.3 26.7 - - + -
87C TRP* 3.6 43.7 - + + -
95C TYR* 1.3 73.4 - - - +
97C ILE* 1.3 83.4 + - - +
98C SER* 3.8 12.2 + - - -
114C MET* 3.7 32.8 - - + -
205C ILE* 3.4 4.0 - - - +
206C CYS* 2.7 39.7 + - + +
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Residues in contact with ILE 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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95C TYR* 5.4 4.9 - - + +
96C PHE* 1.3 90.2 - - - +
98C SER* 1.3 64.2 + - - +
99C THR* 3.8 8.9 + - + +
130C ILE* 5.6 0.7 - - + +
133C ASN* 4.2 24.9 - - + +
134C LEU* 3.8 22.2 - - + -
135C LYS* 3.7 16.2 - - - +
140C TYR* 3.5 31.9 - - + -
204C SER 3.7 1.6 - - - -
205C ILE* 3.8 22.4 - - + -
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 3.8 19.3 + - - -
97C ILE* 1.3 73.7 - - - +
99C THR* 1.3 59.8 + - - +
100C GLY* 3.4 10.7 + - - -
110C ASN* 4.9 12.5 + - - +
114C MET* 5.1 7.1 - - - +
203C LYS* 3.3 9.4 - - - +
204C SER* 2.8 50.7 + - - +
206C CYS* 5.2 4.7 - - - -
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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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137B ASN* 4.5 8.3 + - - +
203B LYS* 4.9 4.9 + - - -
97C ILE* 3.8 10.0 + - + +
98C SER* 1.3 72.2 + - - +
100C GLY* 1.3 65.0 + - - +
101C MET* 3.8 2.4 + - - +
135C LYS* 4.1 27.1 - - - +
203C LYS* 3.4 29.4 - - + +
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Residues in contact with GLY 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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137B ASN* 3.8 23.5 - - - +
98C SER* 3.4 10.9 + - - +
99C THR* 1.3 82.3 + - - +
101C MET* 1.3 60.3 + - - -
102C GLN* 3.9 7.8 + - - +
202C GLN 3.5 1.7 - - - +
203C LYS* 3.4 18.4 - - - -
204C SER* 4.6 1.4 + - - -
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Residues in contact with MET 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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101B MET* 3.9 17.7 - - + +
136B ARG 5.4 0.5 - - - +
137B ASN* 2.7 26.9 + - - +
138B SER* 3.9 9.6 - - - +
139B SER* 3.5 39.9 - - - +
202B GLN* 3.8 11.2 - - - +
203B LYS* 4.0 28.7 - - - +
99C THR 4.5 3.1 - - - +
100C GLY* 1.3 72.3 - - - -
102C GLN* 1.3 63.3 + - - +
201C PRO* 3.6 36.1 - - + +
202C GLN 3.2 6.1 - - - +
203C LYS* 4.1 20.6 - - + +
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Residues in contact with GLN 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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137B ASN* 6.4 0.9 - - + -
100C GLY* 3.9 6.2 + - - +
101C MET* 1.3 82.8 - - - +
103C SER* 1.3 72.1 + - - +
106C LYS* 3.5 33.4 - - + +
107C SER* 3.4 9.2 + - - +
110C ASN* 2.1 43.4 + - - +
141C PHE* 3.2 3.5 - - - -
201C PRO* 3.6 9.9 - - - -
202C GLN 2.9 26.5 + - - +
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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