Contacts of the strand formed by residues 396 - 400 (chain B) in PDB entry 1EOB
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 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.1 11.4 - - + -
351B PHE* 3.9 40.8 - - + -
356B PHE* 3.8 30.3 - - + -
394B ASN 3.8 1.8 + - - -
395B ALA* 1.3 70.0 - - - +
397B VAL* 1.3 64.5 + - - +
398B GLU* 3.8 38.7 - - + +
428B ARG* 4.5 4.3 - - + -
429B MET 3.6 9.6 - - - +
430B LEU* 3.8 4.9 - - + -
464B SER 3.4 1.2 - - - +
465B LEU* 3.3 8.0 - - - +
466B ILE* 2.9 44.8 + - + +
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Residues in contact with VAL 397 (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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384B VAL* 4.8 4.3 - - + -
395B ALA 4.1 3.4 - - - +
396B LEU* 1.3 76.3 - - - +
398B GLU* 1.3 63.7 + - - +
399B VAL* 4.2 12.3 - - + -
428B ARG* 3.0 5.4 - - - +
429B MET* 2.8 66.2 + - + +
431B THR* 4.0 26.2 - - + -
437B TYR* 4.9 14.4 - - + -
439B PHE* 5.9 0.2 - - + -
463B PHE* 5.0 3.4 - - + -
464B SER 3.4 6.5 - - - +
465B LEU* 4.1 24.7 - - + -
525B ILE* 5.3 5.6 - - + -
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY 4.1 10.4 - - - +
21A LEU* 3.3 20.3 - - + +
31A PHE* 6.0 1.1 - - + -
35A LEU* 3.7 12.3 - - - +
94A ARG* 2.8 45.0 + - - -
396B LEU* 3.8 25.5 - - + +
397B VAL* 1.3 78.3 - - - +
399B VAL* 1.3 62.2 + - - +
400B TRP* 3.9 2.7 - - - -
427B GLY 3.6 6.7 - - - +
428B ARG* 4.0 16.5 + - + -
463B PHE* 3.1 4.3 - - - +
464B SER* 2.8 45.1 + - - +
466B ILE* 4.5 1.9 - - - +
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY* 4.0 3.1 - - - -
363B LEU* 4.5 9.0 - - + -
397B VAL* 4.2 13.7 - - + -
398B GLU* 1.3 79.9 - - - +
400B TRP* 1.3 67.5 + - - +
426B CYS* 3.3 2.4 - - - +
427B GLY* 3.0 44.8 + - - +
429B MET* 4.3 8.1 - - + -
439B PHE* 4.2 37.0 - - + -
461B ILE* 4.0 9.6 - - + -
462B HIS 3.0 13.5 - - - +
463B PHE* 3.9 13.5 - - + -
478B PHE* 5.4 1.1 - - + -
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Residues in contact with TRP 400 (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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13A GLY* 3.5 20.0 + - - -
16A TYR* 3.6 18.2 + - - +
17A VAL* 3.6 34.2 - - + +
19A ILE* 3.8 7.2 - - + -
20A GLY* 3.2 34.3 - - - +
21A LEU* 4.0 17.9 - - + -
363B LEU* 5.5 0.2 - - - -
398B GLU 3.9 14.6 - - - -
399B VAL* 1.3 83.8 - - - +
401B GLN* 1.3 62.2 + - - +
408B TYR* 4.7 7.2 - + - -
425B GLY 3.0 12.8 - - - +
461B ILE* 4.0 1.3 - - - -
462B HIS* 2.9 77.3 + + + +
463B PHE 4.4 1.1 - - - -
464B SER* 4.1 5.6 - - - -
475B ILE* 4.3 20.0 - - + -
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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