Contacts of the strand formed by residues 39 - 45 (chain B) in PDB entry 2E4Y
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 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B GLY 3.1 0.2 - - - -
38B ASP* 1.3 95.1 - - - +
40B VAL* 1.3 64.3 + - - +
86B LEU* 5.0 0.7 - - + -
89B VAL* 3.6 21.5 - - + -
90B LYS 3.3 2.0 + - - -
91B LEU* 3.4 15.3 - - + +
92B GLY 2.7 23.4 + - - -
141B LEU* 5.1 11.0 - - + -
143B ALA* 4.4 9.0 - - + -
404B LEU* 3.4 42.6 - - + -
418B LEU* 3.4 30.7 - - + -
422B MET* 5.2 7.0 - - + +
423B LYS 6.0 0.2 - - - +
425B LEU* 4.8 14.4 - - + -
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Residues in contact with VAL 40 (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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35B ILE 4.7 0.2 - - - +
37B GLY 4.3 14.8 - - - +
39B LEU* 1.3 82.1 - - - +
41B LEU* 1.3 71.4 + - - +
92B GLY* 3.2 22.4 - - - +
93B VAL* 3.7 15.7 - - - +
94B HIS 3.9 1.8 - - - +
140B LEU* 3.9 33.0 - - + -
141B LEU* 3.6 23.3 + - + +
142B ILE* 3.6 11.7 - - + -
143B ALA* 2.7 37.2 + - - +
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Residues in contact with LEU 41 (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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40B VAL* 1.3 81.5 - - - +
42B GLY* 1.3 66.8 + - - +
72B MET* 4.0 9.3 - - + +
76B ILE* 3.8 15.7 - - + -
91B LEU* 3.8 31.2 - - + -
92B GLY 2.8 13.6 + - - +
93B VAL* 3.3 5.5 - - - +
94B HIS 3.0 21.7 + - - -
143B ALA* 4.4 6.7 - - + -
144B GLY 3.3 16.6 - - - +
146B ILE* 4.8 7.4 - - + -
397B VAL* 4.4 13.9 - - + +
400B MET* 3.2 36.6 - - + -
401B ALA 5.5 0.2 - - - +
404B LEU* 4.5 6.3 - - + -
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Residues in contact with GLY 42 (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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41B LEU* 1.3 77.7 - - - +
43B GLY* 1.3 57.9 + - - -
72B MET* 3.8 3.4 - - - +
94B HIS 3.2 8.1 - - - -
112B PHE* 3.4 24.0 - - - -
142B ILE* 4.0 7.2 - - - +
144B GLY 2.8 13.2 + - - -
145B VAL* 4.2 6.5 - - - -
146B ILE* 3.0 27.4 + - - +
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Residues in contact with GLY 43 (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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42B GLY* 1.3 74.0 - - - -
44B LEU* 1.3 65.7 + - - +
45B PHE* 4.1 5.6 - - - -
72B MET* 4.2 6.1 - - - -
94B HIS 2.7 13.9 + - - +
95B ILE* 3.9 14.8 - - - -
96B LEU 2.7 31.0 + - - +
112B PHE* 3.8 4.2 - - - -
146B ILE 3.4 7.0 - - - -
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Residues in contact with LEU 44 (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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43B GLY* 1.3 82.2 - - - +
45B PHE* 1.3 65.5 + - - +
46B PRO* 4.5 0.4 - - - +
96B LEU* 3.5 15.3 - - + +
98B THR* 3.7 24.5 - - + -
105B ALA* 4.9 0.9 - - + +
108B GLN* 4.9 5.2 - - + -
109B SER* 3.5 22.9 - - - +
112B PHE* 3.7 22.7 - - + -
145B VAL* 4.3 13.7 - - + -
146B ILE 3.1 7.3 + - - -
147B GLY* 3.7 12.2 - - - -
148B GLY* 3.7 16.9 + - - +
149B SER 4.8 0.2 + - - -
153B VAL* 5.0 1.8 - - + -
157B VAL* 3.9 25.4 - - + -
171B TYR* 2.8 18.0 + - - -
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Residues in contact with PHE 45 (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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44B LEU* 1.3 82.9 - - - +
46B PRO* 1.3 62.1 - - + +
47B ILE* 2.7 30.1 + - + +
65B GLY 4.5 5.4 - - - +
68B ARG* 3.2 30.3 - - + -
69B LEU* 3.6 17.9 - - + -
72B MET* 3.6 40.2 - - + -
95B ILE* 3.5 32.1 - - + -
96B LEU 3.2 5.3 + - - -
97B ASP* 3.1 5.9 - - - +
98B THR* 2.8 22.8 + - - +
146B ILE* 4.5 2.0 - - + -
171B TYR* 3.3 33.2 - + - -
393B VAL* 4.5 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