Contacts of the strand formed by residues 136 - 143 (chain C) in PDB entry 6BW4
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 ASN 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ASN* 5.0 4.6 - - - +
124A GLU* 4.4 2.9 - - - +
125A GLY* 3.4 33.8 + - - +
126A GLU* 5.4 1.4 + - - -
145A PRO* 5.2 1.8 - - - +
133C MET* 3.0 18.7 + - - +
135C GLN* 1.3 80.9 - - - +
137C PRO* 1.3 63.8 - - - +
138C CYS* 3.1 24.4 + - - +
139C ILE* 2.9 50.3 + - + +
153C ASP* 5.3 2.4 + - - -
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Residues in contact with PRO 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 4.1 29.4 - - + +
146A SER* 5.7 8.5 - - - -
50C LEU* 3.9 12.4 - - + +
51C PRO* 4.1 24.0 - - + -
52C ASP* 6.1 0.2 - - - +
132C TYR* 3.6 30.8 - - + +
133C MET 3.1 8.7 - - - +
134C PRO 4.2 4.5 - - - +
136C ASN* 1.3 84.6 - - - +
138C CYS* 1.3 65.1 + - - +
139C ILE 3.2 1.3 + - - -
140C ILE* 4.4 1.0 - - - +
154C TYR* 3.6 14.4 + - - -
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Residues in contact with CYS 138 (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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145A PRO* 3.9 7.9 - - + -
146A SER* 3.6 33.2 - - - -
136C ASN* 3.1 16.3 + - - +
137C PRO* 1.3 77.5 - - - +
139C ILE* 1.3 58.9 + - - +
140C ILE 3.8 0.3 + - - -
152C PHE 3.4 1.9 - - - +
153C ASP* 3.4 21.2 - - - +
154C TYR* 2.9 46.1 + - - +
155C THR* 3.6 24.2 - - + -
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 5.6 4.0 - - - +
74A ASP* 5.3 9.4 - - - +
131C ARG 4.1 0.2 - - - +
132C TYR* 3.3 3.8 - - - +
133C MET* 2.8 61.0 + - + +
136C ASN* 2.9 39.8 + - + +
138C CYS* 1.3 75.6 - - - +
140C ILE* 1.3 60.0 + - - +
141C ALA 4.4 0.2 + - - -
151C VAL* 3.5 27.1 - - + -
152C PHE 3.4 2.0 - - - -
153C ASP* 3.7 33.9 - - + +
185C TRP* 4.0 5.4 - - + -
207C ILE* 4.5 3.1 - - + -
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Residues in contact with ILE 140 (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 VAL* 4.0 14.6 - - + -
79C LEU* 4.0 27.4 - - + -
81C ILE* 3.7 21.3 - - + -
130C ALA* 4.1 16.4 - - + -
131C ARG 3.5 7.6 - - - +
132C TYR* 4.1 13.5 - - + -
137C PRO 4.4 2.7 - - - +
138C CYS 4.3 2.9 - - - +
139C ILE* 1.3 77.9 - - - +
141C ALA* 1.3 73.0 + - - +
142C THR* 4.2 0.4 - - + -
150C LEU 3.8 0.5 - - - +
151C VAL* 3.4 2.3 - - - -
152C PHE* 2.7 44.8 + - + +
154C TYR* 3.7 30.5 - - + -
185C TRP* 4.6 2.0 - - - -
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Residues in contact with ALA 141 (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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130C ALA* 3.2 4.7 - - - -
131C ARG 2.9 31.5 + - - -
140C ILE* 1.3 74.5 - - - +
142C THR* 1.3 62.1 + - - +
149C VAL* 4.8 0.4 - - + -
150C LEU 3.2 8.5 - - - +
151C VAL* 4.5 2.5 - - + +
183C LEU* 3.4 18.4 - - + +
185C TRP* 3.6 27.8 - - + +
193C LEU* 3.8 20.6 - - + -
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Residues in contact with THR 142 (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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79C LEU* 4.1 19.1 - - + -
123C HIS* 2.8 31.5 + - + +
127C VAL* 4.3 4.3 - - + -
129C ARG 3.1 8.5 - - - -
130C ALA* 4.1 14.8 - - + -
140C ILE* 4.2 1.6 - - + -
141C ALA* 1.3 80.9 - - - +
143C LYS* 1.3 62.7 + - - +
144C THR* 4.1 0.3 + - - +
149C VAL* 3.4 8.7 - - - +
150C LEU* 2.8 47.4 + - - +
152C PHE* 4.1 17.0 - - + -
183C LEU* 4.2 2.0 - - - -
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Residues in contact with LYS 143 (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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123C HIS* 4.3 0.7 - - - -
126C GLU 3.7 2.1 - - - +
127C VAL* 3.8 3.3 - - - -
128C ASN* 2.9 35.5 + - + -
129C ARG* 2.9 10.9 + - + +
142C THR* 1.3 73.8 - - - +
144C THR* 1.3 61.8 + - - +
147C SER 5.6 0.8 + - - -
148C ASP 4.7 1.6 - - - +
149C VAL* 3.9 16.0 - - + +
176C HIS* 3.9 11.1 - - - -
178C LYS 5.3 0.8 + - - -
179C GLU* 4.9 0.4 - - - +
180C GLY* 3.3 42.3 - - - +
181C TYR 3.6 16.4 - - - +
182C GLY 3.8 7.9 - - - +
183C LEU* 4.0 19.3 - - + -
195C SER* 2.5 30.1 + - - +
196C ALA 3.0 18.1 + - - -
197C SER* 4.7 0.8 - - - -
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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