Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 3CBG
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLN* 3.2 22.9 - - + +
64A VAL 3.5 27.6 - - - -
65A LEU* 3.7 35.2 - - + -
89A ILE* 3.7 32.8 - - + -
128A LEU* 4.4 10.3 - - + -
135A PRO* 4.4 18.8 - - + -
136A GLU* 1.3 74.4 - - - +
138A ASP* 1.3 61.8 + - - +
139A LEU 3.8 11.7 - - - +
140A ILE* 4.1 9.0 - - + -
159A LEU* 2.9 34.3 + - + +
160A LEU* 3.3 6.5 - - - +
161A ARG* 3.1 25.2 + - - +
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Residues in contact with ASP 138 (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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59A THR* 5.0 4.1 - - + +
60A GLY 5.2 1.1 - - - -
61A ALA* 3.7 23.6 - - + -
62A LYS* 2.8 29.6 + - - +
63A GLN* 2.6 25.7 + - - +
136A GLU 5.0 1.4 - - - +
137A PHE* 1.3 74.8 - - - +
139A LEU* 1.3 57.2 + - - +
160A LEU* 3.8 1.6 - - - -
161A ARG* 2.7 41.7 + - - +
164A GLY* 3.1 5.7 - - - -
165A LEU* 2.8 24.9 + - - +
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Residues in contact with LEU 139 (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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52A LEU* 5.5 4.7 - - + +
55A LEU* 4.5 19.3 - - + +
56A ILE* 4.2 16.6 - - + -
59A THR* 5.0 6.1 - - + -
61A ALA* 4.4 11.2 - - + -
63A GLN 3.3 2.9 + - - +
64A VAL* 3.3 21.9 - - + -
65A LEU 3.0 22.7 + - - -
78A MET* 4.4 12.6 - - - -
137A PHE* 3.8 0.3 - - - +
138A ASP* 1.3 82.5 - - - +
140A ILE* 1.3 80.4 + - - +
141A PHE* 4.0 4.5 - - + +
160A LEU* 4.1 0.4 - - - -
165A LEU* 3.2 34.3 - - + +
167A VAL* 4.4 12.3 - - + -
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.3 36.6 - - + +
67A ILE* 4.6 5.2 - - + -
137A PHE* 4.1 4.5 - - + -
139A LEU* 1.3 83.0 - - - +
141A PHE* 1.3 61.9 + - - +
142A ILE* 3.9 20.4 + - + -
156A GLY* 3.1 36.3 - - - +
159A LEU 4.5 4.5 - - - +
160A LEU* 3.8 17.5 - - + +
165A LEU 3.0 6.9 + - - +
166A MET* 3.2 24.9 - - + +
167A VAL* 2.8 29.8 + - - +
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Residues in contact with PHE 141 (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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44A ILE* 3.8 17.3 - - + -
52A LEU* 4.2 16.2 - - + -
64A VAL* 5.6 0.2 - - + -
65A LEU 2.8 11.4 + - - +
66A GLU* 3.4 21.5 - - - -
67A ILE 2.9 29.5 + - - +
74A SER* 3.8 23.1 - - - -
78A MET* 4.3 21.5 - - + -
139A LEU* 4.0 8.8 - - + +
140A ILE* 1.3 71.3 - - - +
142A ILE* 1.3 59.4 + - - +
143A ASP* 3.5 34.1 - - + -
167A VAL* 3.4 31.4 - - + -
169A ASP* 3.9 18.6 - - + -
214A MET* 5.2 2.9 - - + -
301A SAH 3.9 0.7 - - - -
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Residues in contact with ILE 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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67A ILE* 3.9 14.1 - - + -
140A ILE* 4.1 13.5 - - + +
141A PHE* 1.3 71.0 - - - +
143A ASP* 1.3 64.5 + - - +
144A ALA 4.8 0.2 - - - +
149A TYR* 3.7 34.1 + - + +
152A TYR* 3.8 22.7 - - + +
153A TYR* 3.8 33.9 - - + +
166A MET* 4.1 22.9 - - + -
167A VAL 2.9 13.3 + - - +
168A ILE* 3.6 13.5 - - + -
169A ASP 3.1 25.8 + - - -
193A PHE* 5.9 0.2 - - + -
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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