Contacts of the strand formed by residues 103 - 109 (chain A) in PDB entry 3BMW
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 ALA 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLN* 3.8 7.4 - - - +
80A VAL* 3.6 21.8 - - + -
81A GLU 3.5 5.8 - - - -
82A ASN* 3.7 3.6 - - - +
101A TYR 3.6 2.6 + - - -
102A TRP* 1.3 75.6 - - - +
104A ARG* 1.3 60.0 + - - +
105A ASP 4.6 0.2 - - - +
106A PHE* 3.5 36.1 - - + -
141A HIS 4.7 0.9 - - - +
142A THR* 3.1 33.4 + - - +
143A SER* 4.2 4.0 + - - -
157A ARG 4.5 0.2 - - - +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 2.8 38.0 + - - +
82A ASN 3.4 24.7 - - - +
83A ILE* 4.2 10.5 - - + -
84A TYR* 3.6 23.4 - - - -
102A TRP 3.6 0.8 + - - -
103A ALA* 1.3 75.8 - - - +
105A ASP* 1.3 51.7 + - - +
106A PHE 4.3 0.2 - - - -
154A GLU* 3.0 20.0 + - - +
157A ARG 3.8 15.0 - - - +
158A LEU* 3.6 8.6 - - - +
159A TYR* 2.8 73.4 + - + +
701A SO4 2.8 27.7 + - - -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 3.4 2.0 - - - +
81A GLU* 3.3 46.8 + - + +
103A ALA* 3.8 0.8 - - - +
104A ARG* 1.3 80.4 - - - +
106A PHE* 1.3 58.8 + - - +
107A LYS* 3.1 17.7 + - - +
108A ARG* 3.3 17.3 - - - +
159A TYR* 3.1 23.5 - - + +
161A ASN* 3.1 17.6 + - - -
162A GLY* 2.8 30.0 + - - -
211A TYR* 3.5 1.7 + - - -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLN* 3.4 26.7 - - - -
80A VAL* 3.6 11.5 - - + +
103A ALA* 3.5 23.8 - - + -
105A ASP* 1.3 71.2 - - - +
107A LYS* 1.3 58.0 + - - +
108A ARG 3.5 0.7 - - - -
137A PHE* 3.7 18.6 - + + -
138A ALA 3.5 27.1 - - - -
139A PRO* 4.3 5.6 - - + -
141A HIS 3.6 9.2 - - - -
142A THR* 4.4 2.7 - - + -
158A LEU* 3.8 17.0 - - + -
201A LEU* 4.2 18.2 - - + -
211A TYR* 2.9 31.8 + + + +
212A LEU* 4.5 4.5 - - + -
215A ALA* 3.7 20.6 - - + +
219A TRP* 2.9 28.1 + - - -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP* 3.1 11.1 + - - +
106A PHE* 1.3 80.4 - - - +
108A ARG* 1.3 63.4 + - - +
116A PHE* 3.3 20.7 - - - -
160A ASP* 2.8 35.1 + - - +
161A ASN* 4.2 18.5 - - + +
211A TYR* 3.9 21.2 - - + +
214A SER* 3.3 36.6 + - - -
215A ALA* 3.9 18.6 - - + +
218A VAL* 4.1 20.0 - - + +
219A TRP* 4.7 1.8 - - - +
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 3.1 10.6 - - - +
81A GLU* 2.9 38.0 + - + -
105A ASP* 3.3 24.4 + - - +
107A LYS* 1.3 81.8 - - - +
109A THR* 1.3 67.2 + - - +
116A PHE* 4.0 10.5 - - + -
161A ASN* 3.1 37.2 + - - +
162A GLY* 3.6 21.2 - - - -
219A TRP* 3.7 3.2 - - - -
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TRP* 4.0 8.7 - - + -
79A PRO 3.4 7.9 - - - -
81A GLU* 3.4 14.9 - - - +
108A ARG* 1.3 77.7 - - - +
110A ASN* 1.3 63.0 + - - +
111A PRO* 3.3 12.3 - - - +
114A GLY 2.8 23.3 + - - +
115A SER* 3.8 8.4 - - - -
116A PHE* 3.6 51.5 + - + +
119A PHE* 5.1 0.2 - - + -
219A TRP* 3.9 9.0 - - + -
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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