Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 2EBJ
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 VAL 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.3 9.9 - - + +
63A HIS* 4.4 4.9 - - + -
111A ARG* 2.8 50.4 + - - +
112A PHE* 3.8 1.0 - - - +
143A PHE* 3.8 19.0 - - + -
146A SER* 3.8 24.0 - - - +
147A LEU* 3.5 21.3 - - + -
150A LEU* 3.9 23.3 - - + -
154A VAL 3.5 11.8 + - - +
155A PRO* 1.3 79.3 - - - +
157A GLY* 1.3 64.1 + - - +
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Residues in contact with GLY 157 (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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61A VAL 3.0 9.3 + - - +
62A LEU* 3.6 7.3 - - - -
63A HIS* 3.0 25.1 + - - +
76A GLU 5.6 0.2 - - - -
110A ALA* 5.1 0.7 - - - -
112A PHE* 3.8 26.7 - - - +
143A PHE* 3.6 11.0 - - - -
156A VAL* 1.3 77.2 - - - +
158A PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.5 4.5 - + - -
62A LEU* 4.1 0.6 - - - +
63A HIS* 3.2 33.4 - + + -
64A LEU 3.7 4.3 - - - -
65A GLY 3.7 27.6 - - - -
75A LEU* 3.6 7.4 - - - +
76A GLU* 2.9 35.6 + - + +
134A ALA* 5.0 1.3 - - + -
139A CYS* 3.4 47.1 - - + -
142A ALA* 5.0 0.7 - - + -
143A PHE* 3.7 36.3 - + + -
157A GLY* 1.3 73.2 - - - -
159A LEU* 1.3 66.3 - - - +
160A HIS* 3.5 36.1 - + - -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.4 6.9 - - + +
63A HIS 2.9 8.7 + - - -
64A LEU* 3.4 18.8 - - + +
65A GLY 3.3 20.1 + - - -
73A LEU* 4.0 10.8 - - + -
74A THR 3.4 11.9 - - - +
75A LEU* 3.9 11.0 - - + -
121A TRP* 3.5 30.3 - - + -
158A PHE* 1.3 77.6 - - - +
160A HIS* 1.3 68.1 + - - +
161A LEU* 3.4 29.0 + - + +
185A VAL* 4.0 20.0 - - + -
188A ALA* 4.2 13.9 - - + -
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Residues in contact with HIS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 3.4 17.9 - - - -
66A LEU 3.7 8.7 + - - -
67A ALA* 3.7 25.1 - - + -
70A ARG* 3.6 8.2 + - - +
72A VAL 4.6 0.9 - - - +
73A LEU* 3.8 4.0 - - - -
74A THR* 3.0 44.4 + - - +
76A GLU* 2.7 26.4 + - - +
134A ALA* 3.6 29.1 + - + -
139A CYS* 3.7 16.2 - - + +
158A PHE* 3.5 22.7 - + - -
159A LEU* 1.3 76.5 - - - +
161A LEU* 1.3 58.9 + - - +
162A PRO* 4.0 0.2 - - - +
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Residues in contact with LEU 161 (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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17A PRO* 3.9 4.0 - - + -
18A SER* 3.4 41.7 - - - +
21A LEU* 3.8 23.1 - - + -
64A LEU* 4.3 7.6 - - + -
65A GLY 2.8 15.9 + - - +
66A LEU* 3.3 3.2 - - - +
67A ALA* 2.8 29.2 + - - -
73A LEU* 3.7 9.2 - - + -
159A LEU* 3.4 29.4 - - + +
160A HIS* 1.3 72.4 - - - +
162A PRO* 1.3 69.7 - - - +
181A GLN* 3.2 28.5 - - - +
185A VAL* 4.3 5.6 - - + -
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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