Contacts of the strand formed by residues 132 - 137 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B THR 3.9 0.2 - - - +
124B HIS* 3.7 3.1 - - - -
125B PHE* 2.9 56.3 + - + +
130B ASN* 3.2 24.5 - - + +
131B PRO* 1.3 77.4 - - + +
133B VAL* 1.3 70.8 + - - +
134B ARG 4.3 0.4 - - - -
156B ALA* 4.6 15.0 - - + -
157B PHE* 3.2 24.2 - - - +
158B LEU* 4.4 11.0 - - + +
159B GLN* 4.0 3.4 - - - +
214B ARG* 5.9 2.5 - - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 4.9 8.5 - - + -
96B LEU* 5.0 4.9 - - + -
122B ILE* 3.7 32.1 - - + -
123B THR 3.3 4.0 - - - +
124B HIS* 4.6 5.8 - - + -
132B LEU* 1.3 79.5 - - - +
134B ARG* 1.3 66.2 + - - +
156B ALA* 3.6 0.4 - - - -
157B PHE* 2.9 36.5 + - - +
159B GLN* 4.6 6.7 - - + +
162B VAL* 4.4 18.6 - - + -
163B LEU* 4.2 18.6 - - + -
174B PHE* 3.9 24.5 - - + -
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.7 0.6 - - - -
123B THR* 2.7 52.8 + - - +
125B PHE* 3.9 33.4 - - + -
132B LEU 4.3 0.2 - - - -
133B VAL* 1.3 78.3 - - - +
135B VAL* 1.3 58.0 + - - +
136B ASN* 3.3 33.4 + - - +
154B ASN* 3.3 28.8 + - - +
155B GLN 3.3 24.7 - - - +
156B ALA* 3.6 17.7 - - + -
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 5.0 5.8 - - + -
96B LEU* 4.1 18.8 - - + +
98B LEU* 5.1 2.5 - - + -
120B TYR* 4.3 13.0 - - + -
121B THR 3.3 11.9 - - - +
122B ILE* 3.7 17.7 - - + -
133B VAL* 4.3 1.0 + - - +
134B ARG* 1.3 70.1 - - - +
136B ASN* 1.3 71.4 + - - +
149B LEU* 3.4 27.8 - - + +
154B ASN* 3.2 2.8 - - - -
155B GLN* 2.9 45.7 + - + +
157B PHE* 4.2 11.4 - - + -
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Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PRO* 5.0 3.2 - - - +
120B TYR* 3.3 6.9 - - - +
121B THR* 2.9 47.8 + - - +
123B THR* 3.5 21.6 - - - +
134B ARG* 3.3 39.4 + - - +
135B VAL* 1.3 82.3 - - - +
137B ARG* 1.3 62.4 + - - +
138B LEU* 3.9 5.4 + - + +
153B GLY 3.4 6.5 - - - +
154B ASN* 4.0 5.6 - - + +
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA* 3.0 25.9 + - - +
117B LEU 4.9 2.4 + - - -
118B ALA* 3.7 17.3 - - + +
120B TYR* 3.5 27.0 + - + -
136B ASN* 1.3 66.6 - - - +
138B LEU* 1.3 74.4 + - - +
139B GLY 3.9 7.2 + - - +
140B PRO* 2.6 33.7 + - - +
141B GLY* 3.9 3.8 - - - -
142B ILE* 3.4 24.2 - - - +
149B LEU* 3.5 25.9 - - + +
150B LEU* 3.4 22.8 - - - +
153B GLY* 2.4 39.9 + - - +
61C HIS* 5.5 3.6 + - - +
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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