Contacts of the strand formed by residues 557 - 564 (chain A) in PDB entry 1E8U
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 ARG 557 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ALA* 2.9 24.7 - - - +
166A PRO* 3.6 23.4 - - + +
173A THR* 3.3 9.4 - - - +
546A ALA 3.5 0.9 - - - +
547A GLU* 4.2 0.9 - - - -
548A ILE 3.0 31.4 + - - +
555A GLU 4.2 5.8 - - - +
556A PHE* 1.3 77.0 - - - +
558A ILE* 1.3 72.0 + - - +
559A VAL* 3.6 14.7 + - + +
169B GLY* 2.9 32.6 + - - -
170B SER* 4.4 3.2 - - - +
552B LEU 5.7 0.2 + - - -
553B PHE* 3.6 31.7 + - + +
554B GLY* 3.9 21.1 - - - +
555B GLU* 5.2 0.4 - - - +
557B ARG* 5.8 4.2 - - - +
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Residues in contact with ILE 558 (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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163A ILE* 3.7 22.2 - - + +
164A PRO 4.9 2.1 - - - +
165A ALA* 6.0 0.2 - - - -
173A THR* 2.9 23.5 + - - +
174A ARG* 3.7 20.9 - - - +
176A PRO* 3.5 15.5 - - + -
187A TYR* 3.2 17.7 - - - +
189A HIS* 3.2 37.0 - - + +
545A ILE* 3.3 27.4 - - + -
546A ALA 3.4 6.7 - - - +
547A GLU* 4.2 11.7 - - + -
557A ARG* 1.3 77.6 - - - +
559A VAL* 1.3 63.8 + - - +
560A PRO* 4.1 1.4 - - - +
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Residues in contact with VAL 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A HIS* 6.1 4.5 - - + -
160A LEU 5.9 0.2 - - - +
544A SER 3.7 1.6 - - - +
545A ILE* 3.7 1.5 - - - -
546A ALA* 2.8 34.7 + - - +
548A ILE* 4.2 18.8 - - + -
557A ARG* 4.0 23.1 - - + +
558A ILE* 1.3 81.6 - - - +
560A PRO* 1.3 78.7 - - + +
561A LEU* 3.8 16.5 + - + +
552B LEU* 3.8 33.4 - - + +
553B PHE* 5.6 1.6 - - + -
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Residues in contact with PRO 560 (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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159A HIS* 4.2 4.0 - - - -
160A LEU* 3.5 45.6 + - + +
162A PHE* 3.7 23.3 - - + -
163A ILE* 3.8 34.8 - - + +
543A LEU* 4.0 9.6 - - + -
544A SER 3.6 5.2 - - - +
545A ILE* 4.3 3.8 - - + -
558A ILE 4.1 1.3 - - - +
559A VAL* 1.3 94.1 - - + +
561A LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 561 (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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156A PHE* 4.0 33.2 - - + -
158A GLU 4.1 3.4 - - - -
159A HIS* 4.9 6.5 - - + -
160A LEU* 4.9 0.7 - - - -
490A THR* 5.5 0.7 - - + +
503A SER* 5.4 0.2 - - - +
517A VAL* 3.9 32.1 - - + -
542A CYS 4.5 0.2 - - - -
543A LEU* 3.4 8.4 - - - +
544A SER* 2.7 54.0 + - - +
546A ALA* 4.8 10.3 - - + -
548A ILE* 6.0 1.1 - - + -
559A VAL* 4.2 14.8 - - + +
560A PRO* 1.3 80.4 - - - +
562A LEU* 1.3 61.5 + - - +
563A VAL* 5.5 0.4 - - + -
552B LEU* 3.7 29.6 - - + -
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Residues in contact with LEU 562 (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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156A PHE* 3.3 5.6 - - - -
157A GLN* 2.8 27.6 + - + +
158A GLU* 3.6 42.9 + - - +
160A LEU* 4.3 19.3 - - + -
219A ILE* 4.2 28.9 - - + -
221A PHE* 4.9 3.8 - - + -
532A PHE* 3.9 21.5 - - + -
541A TYR* 4.0 12.6 - - + -
542A CYS 3.4 24.2 - - - +
543A LEU* 4.0 7.4 - - + +
561A LEU* 1.3 76.6 - - - +
563A VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 563 (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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153A PRO* 4.0 11.9 - - + -
154A SER 3.9 19.5 - - - +
155A ALA 4.2 0.7 - - - -
156A PHE* 3.2 41.1 - - + -
157A GLN* 4.1 7.0 - - - -
488A PHE* 3.8 30.1 - - + -
503A SER* 5.3 2.5 - - - +
515A THR* 4.9 0.9 - - + -
541A TYR* 3.3 6.5 - - - +
542A CYS* 2.9 42.2 + - + +
544A SER* 6.2 1.1 - - - -
561A LEU 5.5 0.4 - - - -
562A LEU* 1.3 74.1 - - - +
564A GLU* 1.3 64.5 + - - +
565A ILE* 4.7 1.3 - - + -
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Residues in contact with GLU 564 (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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153A PRO* 3.6 2.4 - - - +
154A SER* 3.0 39.1 + - - +
157A GLN* 3.7 16.4 + - + +
539A LYS* 3.4 39.3 + - + +
540A THR 3.4 13.6 + - - +
541A TYR* 3.7 24.2 + - + -
563A VAL* 1.3 75.4 - - - +
565A ILE* 1.3 71.7 + - - +
566A LEU* 3.6 23.2 + - + +
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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