Contacts of the strand formed by residues 371 - 374 (chain E) in PDB entry 1M54
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 371 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89E MET* 4.2 15.7 - - + -
106E LEU* 3.2 7.9 - - + +
108E LYS* 4.5 2.0 - - + -
240E ILE* 3.7 24.7 - - + -
244E CYS* 3.4 27.6 - - - -
248E LEU* 3.4 31.2 - - + -
250E MET 3.0 8.1 + - - +
251E LEU* 3.1 16.9 - - + -
252E VAL 3.1 22.5 + - - -
369E ARG* 5.3 0.4 - - + -
370E CYS* 1.3 77.1 - - - +
372E VAL* 1.3 73.6 + - - +
373E ILE* 4.6 0.4 - - + -
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Residues in contact with VAL 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E LEU* 3.6 18.2 - - + -
106E LEU 2.9 6.5 + - - +
107E ALA* 3.2 6.4 - - + +
108E LYS* 2.6 33.8 + - - +
252E VAL* 3.7 18.6 - - + +
353E THR* 4.3 7.4 - - - -
354E VAL* 4.2 26.5 - - + +
357E ALA* 3.5 28.7 - - + -
370E CYS* 3.9 2.2 - - - -
371E VAL* 1.3 82.2 - - - +
373E ILE* 1.3 75.7 + - - +
374E LEU* 4.3 2.9 - - + -
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Residues in contact with ILE 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E LYS* 3.7 17.0 - - + +
110E GLU* 5.0 11.0 - - + +
118E VAL* 5.5 5.6 - - + -
236E THR* 6.1 1.8 - - + -
240E ILE* 4.8 0.4 - - + -
251E LEU* 3.9 36.3 - - + -
252E VAL 3.9 10.4 + - - +
253E ALA* 4.4 6.5 - - + -
254E SER* 5.3 5.4 - - - +
260E THR* 5.9 9.0 - - + -
264E ILE* 4.4 15.5 - - + -
353E THR* 3.5 24.6 + - + +
371E VAL* 4.6 3.1 - - + -
372E VAL* 1.3 84.4 - - - +
374E LEU* 1.3 68.7 + - - +
375E PRO* 3.4 28.6 - - + +
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Residues in contact with LEU 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ALA* 4.3 12.6 - - + -
108E LYS 3.0 14.4 + - - +
109E CYS* 4.1 8.3 - - - -
110E GLU 3.2 20.3 + - - -
111E PHE* 3.3 38.1 - - + -
338E LEU* 4.9 0.9 - - + -
344E LEU* 4.0 23.1 - - + -
346E CYS* 4.2 7.4 - - - -
350E ALA* 3.3 27.4 - - + -
354E VAL* 3.6 26.7 - - + -
372E VAL* 4.3 5.8 - - + -
373E ILE* 1.3 82.3 - - - +
375E PRO* 1.3 66.3 - - - +
376E ASP 3.6 2.0 + - - -
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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