Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 3BGD
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 PHE 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.5 36.8 - - + +
60A VAL 3.8 2.9 - - - -
61A PHE* 3.7 25.1 - + + -
80A THR 5.7 0.2 - - - -
82A VAL* 3.6 32.3 - - + -
138A ILE* 3.6 42.6 - - + -
139A GLY 3.6 17.3 - - - -
140A LYS* 1.3 75.7 - - - +
142A ASP* 1.3 62.3 + - - +
143A ARG 3.3 12.3 - - - +
144A ILE* 4.7 4.7 - - + -
168A LEU* 2.8 27.7 + - + +
169A LEU* 3.8 6.1 - - - +
170A ARG* 2.9 32.3 + - - +
173A PHE* 4.4 0.7 - - - +
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Residues in contact with ASP 142 (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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55A GLN* 5.6 1.7 + - - +
57A GLY 4.8 0.9 - - - +
58A LEU* 3.4 31.3 - - + +
59A ARG* 3.0 28.7 + - - +
141A PHE* 1.3 74.1 - - - +
143A ARG* 1.3 73.4 + - + +
170A ARG* 3.1 33.1 + - - +
172A GLU 4.2 9.9 - - - +
173A PHE* 3.2 7.3 - - - +
174A GLN 3.1 23.7 + - - -
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Residues in contact with ARG 143 (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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51A PHE* 2.6 51.1 + - + +
52A LEU* 4.8 5.6 - - + +
53A LYS 5.1 1.0 + - - -
55A GLN* 3.2 26.9 + - - +
58A LEU* 3.8 28.0 - - + +
59A ARG 3.3 1.9 + - - +
60A VAL* 3.3 20.0 - - + -
61A PHE 2.9 22.8 + - - -
141A PHE* 3.3 3.2 - - - +
142A ASP* 1.3 107.3 + - + +
144A ILE* 1.3 66.3 + - - +
169A LEU* 5.3 0.2 - - - -
172A GLU 5.4 0.8 + - - -
173A PHE* 4.5 4.2 - - - +
174A GLN* 3.3 48.1 - - - +
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Residues in contact with ILE 144 (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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51A PHE* 3.5 7.1 - - - -
60A VAL* 5.0 0.2 - - - -
61A PHE* 3.3 31.9 - - + +
63A PRO* 3.7 20.4 - - + -
141A PHE* 4.7 3.4 - - + -
143A ARG* 1.3 78.6 - - - +
145A TRP* 1.3 64.7 + - - +
165A ILE* 3.8 29.4 - - + +
168A LEU* 4.8 6.3 - - + +
169A LEU* 3.6 31.0 - - + -
174A GLN 3.2 7.5 + - - -
175A TYR* 3.6 26.0 - - + -
176A LEU 3.0 27.5 + - - +
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Residues in contact with TRP 145 (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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41A HIS* 3.7 38.8 - + + +
44A LEU* 3.7 32.6 - - + +
51A PHE* 4.8 5.6 - - + -
60A VAL* 4.7 2.0 - - + +
61A PHE 3.1 8.2 + - - +
62A PHE* 3.4 46.3 - + + +
63A PRO* 3.3 18.5 - - - +
68A ALA* 5.8 1.0 - - + +
70A GLU* 4.2 10.7 + - - -
74A PHE* 4.8 6.5 - - + -
144A ILE* 1.3 74.1 - - - +
146A ASP* 1.3 60.0 + - - +
147A ARG* 3.4 34.6 + - + +
176A LEU* 3.5 34.8 - - + -
178A ALA* 4.6 2.0 - - + -
234A LEU* 3.6 31.4 - - + -
300A SAH 5.7 0.4 + - - -
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Residues in contact with ASP 146 (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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63A PRO* 4.1 8.2 - - + +
145A TRP* 1.3 75.0 - - - +
147A ARG* 1.3 60.5 + - - +
149A ALA* 3.0 6.3 + - - +
150A LEU* 2.8 29.2 + - - +
151A VAL 4.9 0.2 + - - -
161A TYR* 2.6 26.6 + - - -
165A ILE* 4.9 0.2 - - - +
175A TYR* 2.7 35.5 + - + -
176A LEU 2.9 16.4 + - - +
177A VAL* 3.3 12.5 - - - +
178A ALA* 2.8 29.6 + - - +
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Residues in contact with ARG 147 (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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35A PHE* 2.8 29.5 + - - +
37A GLN* 3.7 33.9 + - - +
41A HIS* 3.7 27.3 + - + +
63A PRO 4.9 0.4 + - - +
70A GLU* 6.6 0.4 - - - -
145A TRP* 3.4 31.1 + - + +
146A ASP* 1.3 76.2 + - - +
148A GLY* 1.3 66.9 + - - +
149A ALA* 3.0 5.0 + - - +
178A ALA* 4.0 15.5 - - + +
221A ARG* 5.6 3.8 - - - +
232A GLU* 4.8 3.4 + - - +
300A SAH 2.7 62.3 + - - +
301A PM6 3.3 32.3 + - - -
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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