Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 3H44
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 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.8 10.4 - - - +
136A GLY* 1.3 76.1 - - - -
138A SER* 1.3 62.1 + - - +
151A PHE* 3.2 4.9 - - - +
152A ASP* 2.9 43.1 + - - +
431A ARG* 3.1 20.3 + - - -
892A ARG* 5.0 2.0 - - - -
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Residues in contact with SER 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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115A PHE* 3.7 10.4 - - - -
127A TYR* 2.7 31.9 + - - -
128A SER* 6.4 0.9 - - - -
131A LEU* 3.6 15.5 - - - -
137A SER* 1.3 80.9 + - - +
139A ASN* 1.3 69.0 + - - +
150A TYR 2.7 17.9 + - - -
151A PHE* 4.0 0.9 - - - +
431A ARG* 4.0 10.3 + - - +
20C GLN* 5.7 1.0 + - - -
21C VAL* 5.4 2.9 - - - +
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Residues in contact with ASN 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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115A PHE* 4.1 10.2 - - - -
138A SER* 1.3 76.9 + - - +
140A ALA* 1.3 68.3 + - - +
149A TYR* 3.7 0.3 - - - -
150A TYR* 3.0 60.4 + - + +
431A ARG* 4.1 7.9 - - - +
19C ARG* 4.3 6.9 - - - +
20C GLN* 2.6 65.5 + - - +
21C VAL* 3.8 13.8 - - - +
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Residues in contact with ALA 140 (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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111A GLN* 3.5 31.9 - - + +
115A PHE* 3.8 8.5 - - + -
139A ASN* 1.3 85.1 + - - +
141A PHE* 1.3 66.3 + - - +
148A ASN 3.0 16.2 - - - +
149A TYR* 3.7 16.4 - - + -
150A TYR* 4.1 3.4 - - - -
19C ARG* 3.4 23.5 - - - +
20C GLN* 4.4 0.2 - - - +
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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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91A ASP* 5.3 0.7 - - - -
111A GLN* 3.5 3.1 - - - +
140A ALA* 1.3 76.0 - - - +
142A THR* 1.3 65.6 + - - +
143A SER* 4.1 23.1 - - - -
146A HIS* 5.1 4.9 - - + -
147A THR* 3.5 3.8 - - - +
148A ASN* 3.0 70.4 + - + -
150A TYR* 4.1 13.5 - + - -
435A SER* 4.1 7.9 - - - -
17C ARG* 3.7 49.4 - - + +
18C SER 3.2 16.6 - - - +
19C ARG* 4.3 15.7 - - + +
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Residues in contact with THR 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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96A SER* 4.1 8.0 + - - +
107A SER* 3.6 23.8 - - - +
108A HIS* 3.5 25.4 - - + +
111A GLN* 2.7 32.8 + - - +
141A PHE* 1.3 74.7 - - - +
143A SER* 1.3 69.6 + - - +
146A HIS 3.3 2.9 - - - +
147A THR* 3.5 17.7 - - - +
16C LYS 4.9 0.2 - - - +
17C ARG* 3.8 2.3 - - - -
18C SER* 3.0 29.9 + - - -
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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