Contacts of the strand formed by residues 64 - 69 (chain B) in PDB entry 2E9D
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 ALA 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG 3.1 4.0 + - - +
20B HIS* 3.4 32.5 - - + +
21B VAL 3.1 22.7 + - - -
62B ILE* 3.2 10.1 - - - +
63B GLU* 1.3 80.0 - - + +
65B LEU* 1.3 59.8 + - - +
137B LEU* 3.7 4.0 - - - -
138B THR* 3.3 12.3 - - - +
140B ASN* 4.3 0.7 - - - +
186B LEU* 4.0 22.4 - - + -
187B ALA* 5.6 1.6 - - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.3 26.5 - - + +
23B ILE* 3.8 25.6 - - + -
53B ALA* 3.9 15.9 - - + +
54B VAL* 4.0 23.6 - - + -
57B ALA* 3.7 25.6 - - + -
62B ILE* 5.5 0.2 - - + -
64B ALA* 1.3 74.4 - - - +
66B THR* 1.3 62.5 + - - +
67B LEU* 4.0 15.7 - - + -
137B LEU* 3.8 17.2 - - + +
138B THR 2.9 6.2 + - - +
139B LEU* 3.5 8.8 - - + +
140B ASN* 2.8 27.6 + - - +
229B PHE* 4.4 2.9 - - + -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B HIS* 2.8 28.1 + - - -
21B VAL 2.8 11.1 + - - +
22B ALA* 3.4 6.9 - - - -
23B ILE 2.9 29.5 + - - +
65B LEU* 1.3 74.1 - - - +
67B LEU* 1.3 66.0 - - - +
68B TYR 4.1 0.2 + - - -
110B ILE* 4.2 13.5 - - + -
140B ASN* 3.2 23.7 + - + +
183B MET* 3.4 19.7 - - + -
204B PHE* 3.6 25.7 - - + -
205B LEU* 4.5 1.1 - - + -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.7 37.0 - - + -
25B MET* 3.9 23.5 - - + +
50B VAL* 3.8 30.7 - - + +
53B ALA* 5.4 1.8 - - + -
54B VAL* 4.0 9.2 - - + -
65B LEU* 4.0 9.6 - - + -
66B THR* 1.3 76.1 - - - +
68B TYR* 1.3 61.1 + - - +
69B ALA 4.2 0.5 + - - -
139B LEU* 3.8 25.6 - - + -
140B ASN 2.8 13.1 + - - +
141B ILE* 3.8 14.5 - - + +
142B ALA* 2.8 32.7 + - - +
221B TRP* 5.0 3.4 - - + -
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Residues in contact with TYR 68 (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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23B ILE 3.0 10.7 + - - +
24B ILE* 3.9 20.6 - - + -
25B MET* 3.0 28.4 + - - +
67B LEU* 1.3 76.0 - - - +
69B ALA* 1.3 76.7 + - - +
70B PHE* 3.6 23.2 + + - -
142B ALA* 3.4 20.2 - - + -
145B TYR* 4.0 25.9 + + + -
201B ILE 5.0 1.1 - - - -
202B SER 3.6 18.7 + - - -
203B ASN* 4.7 1.4 + - - +
204B PHE* 3.4 45.5 - + + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 3.2 21.3 - - + +
67B LEU 4.1 0.6 + - - -
68B TYR* 1.3 90.7 - - - +
70B PHE* 1.3 61.0 + - - +
71B SER* 3.9 2.6 + - - -
142B ALA* 5.1 5.0 + - - +
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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