Contacts of the strand formed by residues 132 - 137 (chain A) in PDB entry 4LDD
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 LEU 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A THR 3.9 0.2 - - - +
124A HIS* 3.7 3.3 - - - -
125A PHE* 2.9 56.0 + - + +
130A ASN* 3.2 23.8 - - + +
131A PRO* 1.3 77.6 - - + +
133A VAL* 1.3 71.3 + - - +
134A ARG 4.3 0.2 - - - -
156A ALA* 4.6 14.8 - - + -
157A PHE* 3.2 24.0 - - - +
158A LEU* 4.4 10.5 - - + +
159A GLN* 4.0 3.4 - - - +
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Residues in contact with VAL 133 (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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94A ILE* 4.9 8.5 - - + -
96A LEU* 5.0 5.4 - - + -
122A ILE* 3.7 32.3 - - + -
123A THR 3.3 4.0 - - - +
124A HIS* 4.6 6.5 - - + -
132A LEU* 1.3 80.1 - - - +
134A ARG* 1.3 65.2 + - - +
156A ALA* 3.6 0.4 - - - -
157A PHE* 2.9 36.4 + - - +
159A GLN* 4.6 6.4 - - + +
162A VAL* 4.4 18.4 - - + -
163A LEU* 4.2 18.4 - - + -
174A PHE* 3.9 23.6 - - + -
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Residues in contact with ARG 134 (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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122A ILE* 3.7 1.0 - - - -
123A THR* 2.7 52.2 + - - +
125A PHE* 3.9 33.3 - - + -
133A VAL* 1.3 77.6 - - - +
135A VAL* 1.3 59.7 + - - +
136A ASN* 3.3 33.7 + - - +
154A ASN* 3.3 27.8 + - - +
155A GLN 3.3 23.6 - - - +
156A ALA* 3.6 17.0 - - + -
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Residues in contact with VAL 135 (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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75A LEU* 5.0 5.6 - - + -
96A LEU* 4.1 19.7 - - + +
98A LEU* 5.1 2.5 - - + -
120A TYR* 4.3 12.8 - - + -
121A THR 3.3 11.4 - - - +
122A ILE* 3.8 18.4 - - + -
133A VAL* 5.2 0.4 - - - +
134A ARG* 1.3 70.4 - - - +
136A ASN* 1.3 70.5 + - - +
149A LEU* 3.3 30.6 - - + +
154A ASN* 3.2 2.9 - - - -
155A GLN* 2.9 43.8 + - + +
157A PHE* 4.2 10.8 - - + -
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Residues in contact with ASN 136 (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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47A PRO* 5.0 3.2 - - - +
120A TYR* 3.3 6.6 - - - +
121A THR* 2.9 46.8 + - - +
123A THR* 3.5 22.1 - - - +
134A ARG* 3.3 39.0 + - - +
135A VAL* 1.3 81.5 - - - +
137A ARG* 1.3 63.3 + - - +
138A LEU* 3.9 5.8 + - + +
153A GLY 3.4 6.1 - - - +
154A ASN* 4.1 5.4 - - + -
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Residues in contact with ARG 137 (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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114A ALA* 3.0 25.3 + - - +
117A LEU 4.9 2.2 + - - -
118A ALA* 3.7 17.7 - - + +
120A TYR* 3.5 26.5 + - + -
136A ASN* 1.3 67.1 - - - +
138A LEU* 1.3 73.1 + - - +
139A GLY 3.8 7.7 + - - +
140A PRO* 2.6 33.3 + - - +
141A GLY* 3.9 3.8 - - - -
142A ILE* 3.4 24.3 - - - +
149A LEU* 3.5 26.6 - - + +
150A LEU* 3.4 22.0 - - - +
153A GLY* 2.4 39.5 + - - +
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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