Contacts of the strand formed by residues 141 - 145 (chain B) in PDB entry 2NS2
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 3.4 47.3 - - + -
107B MET* 3.6 12.3 - - - -
108B ILE* 3.9 10.3 - - + -
130B VAL* 3.6 16.4 - - + -
132B ALA 3.4 17.5 - - - -
133B ARG* 3.9 19.3 - - + -
139B THR 3.4 19.5 - - - -
140B TRP* 1.3 75.5 - - - +
142B TYR* 1.3 66.7 + - - +
143B ILE* 3.4 4.2 + - - +
152B TYR 3.5 0.2 - - - +
153B MET* 3.3 6.3 - - - -
154B TYR 2.7 37.4 + - - +
156B LEU* 3.8 26.0 - - + -
157B LEU* 4.1 18.8 - - + -
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.8 13.9 - - - +
53B ASP* 4.9 2.2 + - - -
63B LEU* 4.1 15.8 - - + +
72B VAL* 3.9 12.1 - - + +
130B VAL* 3.9 3.5 - - - +
131B LEU* 2.9 29.3 + - + -
132B ALA* 3.0 33.6 + - + +
134B ALA* 3.7 21.9 - - + +
135B PRO* 3.2 33.1 - - + +
141B PHE* 1.3 73.9 - - - +
143B ILE* 1.3 61.6 + - - +
151B LEU* 3.7 22.9 - - + -
152B TYR 3.4 6.3 - - - -
153B MET* 3.9 15.3 - - - -
209B HIS* 6.4 0.7 - + - -
219B PHE* 3.8 27.6 - + - -
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Residues in contact with ILE 143 (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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112B VAL* 5.4 7.0 - - + -
114B HIS* 4.5 8.3 - - + +
128B GLY 5.3 1.3 - - - -
129B MET 3.3 20.0 - - - +
130B VAL* 4.3 7.9 - - + -
131B LEU* 3.9 5.7 - - - +
141B PHE 3.9 5.6 - - - +
142B TYR* 1.3 76.8 - - - +
144B THR* 1.3 68.6 + - - +
145B TYR* 3.6 31.4 - - + +
151B LEU* 3.7 0.5 - - - +
152B TYR* 2.6 61.6 + - + +
154B TYR* 3.8 12.1 - - + -
156B LEU* 3.6 27.6 - - + -
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Residues in contact with THR 144 (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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128B GLY* 3.2 2.9 - - - -
129B MET* 3.0 39.4 + - + +
131B LEU* 3.9 10.5 - - + +
143B ILE* 1.3 76.4 - - - +
145B TYR* 1.3 78.2 + - - +
146B GLU* 5.7 3.4 - - - +
149B PRO* 3.3 9.7 - - + +
150B VAL 2.7 35.9 + - - -
230B VAL* 3.9 31.8 - - + +
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Residues in contact with TYR 145 (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 HIS* 2.8 39.0 + + - -
126B TRP* 3.8 28.7 - + + -
127B ARG 3.6 15.9 - - - +
128B GLY* 3.8 6.7 - - - -
143B ILE* 3.6 21.4 - - + +
144B THR* 1.3 81.6 + - - +
146B GLU* 1.3 64.4 + - - +
147B LYS 4.2 2.2 - - - +
148B ASP* 2.8 44.1 + - + +
149B PRO* 3.0 6.4 - - - +
152B TYR* 3.6 47.3 - + + -
154B TYR* 3.2 21.8 - + - -
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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
------------------------------------------------------------
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