Contacts of the strand formed by residues 93 - 102 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89F SER* 3.2 5.0 - - - -
90F PHE 2.9 32.3 + - - -
91F GLN* 3.4 1.3 - - - +
92F SER* 1.3 86.4 + - - +
94F CYS* 1.3 63.1 + - - +
95F TYR* 3.6 27.3 + - - -
207F LYS* 3.6 22.5 - - - -
208F MET 3.4 9.6 + - - -
209F LYS* 4.4 6.9 + - - -
210F LYS* 3.4 3.9 + - - +
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Residues in contact with CYS 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F CYS* 2.0 51.8 - - + -
84F PRO* 4.5 0.7 - - - -
87F TRP* 3.7 17.7 - - + -
88F THR 3.4 4.5 - - - -
93F SER* 1.3 73.2 - - - +
95F TYR* 1.3 62.1 + - - +
207F LYS* 3.4 5.2 - - - +
208F MET* 2.6 53.2 + - + +
210F LYS* 3.5 24.5 - - - -
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Residues in contact with TYR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F PRO 4.9 0.2 - - - +
87F TRP* 3.2 11.4 - - - -
88F THR* 2.7 45.2 + - - +
90F PHE* 3.7 25.0 + - + -
93F SER* 3.6 32.0 + - - -
94F CYS* 1.3 74.4 - - - +
96F PHE* 1.3 59.2 + - - +
97F ILE* 4.3 6.5 - - + +
119F VAL* 3.7 17.7 - - + -
126F GLU* 2.5 39.1 + - + +
129F PHE* 3.4 24.2 - + + -
130F ILE* 4.2 16.2 - - + -
133F ASN* 6.3 0.9 - - - -
205F ILE* 4.7 5.6 - - + -
206F CYS 3.4 12.6 - - - +
207F LYS* 3.7 12.3 - - + -
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Residues in contact with PHE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F PRO* 4.2 32.8 - - + -
87F TRP* 3.5 31.1 - + + -
95F TYR* 1.3 76.9 - - - +
97F ILE* 1.3 85.7 + - - +
98F SER* 3.5 19.1 + - - -
99F THR 5.6 0.9 - - - -
110F ASN* 5.8 0.2 - - - -
114F MET* 4.0 33.2 - - + -
205F ILE* 3.5 1.4 - - - -
206F CYS* 2.7 44.6 + - + +
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Residues in contact with ILE 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F TYR* 5.3 6.1 - - + -
96F PHE* 1.3 92.1 - - - +
98F SER* 1.3 63.1 + - - +
99F THR* 3.6 4.9 + - - -
130F ILE* 5.2 2.2 - - + +
133F ASN* 3.6 30.7 - - + +
134F LEU* 3.7 21.1 - - + -
135F LYS* 4.2 11.4 - - - +
140F TYR* 3.3 37.7 - - + +
204F SER 3.7 1.8 - - - -
205F ILE* 3.8 21.5 - - + -
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Residues in contact with SER 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F PHE* 3.5 19.7 + - - -
97F ILE* 1.3 73.1 - - - +
99F THR* 1.3 64.1 + - - +
100F GLY* 3.4 8.1 + - - -
110F ASN* 3.0 26.3 + - - -
203F LYS* 3.5 8.1 - - - +
204F SER* 2.7 54.0 + - - +
206F CYS* 4.9 4.0 - - - -
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Residues in contact with THR 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASN* 4.1 17.5 + - - +
138D SER* 5.6 0.2 + - - -
203D LYS* 4.8 4.3 + - - -
96F PHE* 5.6 1.0 - - - -
97F ILE* 3.6 5.9 + - - -
98F SER* 1.3 72.3 + - - +
100F GLY* 1.3 64.8 + - - +
101F MET* 3.9 1.7 + - - +
135F LYS* 4.9 9.9 + - - +
203F LYS* 3.4 32.8 + - - +
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Residues in contact with GLY 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASN* 3.7 24.2 - - - -
98F SER* 3.4 10.6 + - - +
99F THR* 1.3 85.0 - - - +
101F MET* 1.3 61.7 + - - -
102F GLN* 3.8 9.6 + - - +
107F SER* 5.4 0.5 + - - -
202F GLN 3.4 9.7 - - - +
203F LYS* 3.5 8.5 - - - -
204F SER* 4.3 2.1 + - - -
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Residues in contact with MET 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D MET* 3.8 23.8 - - + +
136D ARG 5.4 0.2 - - - +
137D ASN* 2.6 25.0 + - - +
138D SER* 4.0 9.7 - - - -
139D SER* 3.5 35.7 - - - +
202D GLN* 3.9 8.7 - - - +
203D LYS* 4.0 34.5 - - - +
99F THR 4.7 2.2 - - - +
100F GLY* 1.3 71.7 - - - -
102F GLN* 1.3 64.8 + - - +
201F PRO* 3.8 28.0 - - + +
202F GLN 3.2 17.3 - - - +
203F LYS* 3.9 11.9 - - + +
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Residues in contact with GLN 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASN* 6.4 0.7 - - + -
100F GLY* 3.8 7.1 + - - +
101F MET* 1.3 80.4 - - - +
103F SER* 1.3 68.3 + - - +
106F LYS* 3.3 33.9 + - + +
107F SER* 3.4 13.5 + - - +
110F ASN* 3.6 31.1 + - - +
141F PHE* 3.3 4.7 - - - -
201F PRO* 3.6 9.6 - - - -
202F GLN 2.9 25.7 + - - +
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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