Contacts of the strand formed by residues 397 - 403 (chain E) in PDB entry 3RL8
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 PHE 397 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322E LEU 3.7 2.7 - - - +
323E ILE* 4.0 32.1 - - + -
375E ASN* 4.1 12.5 + - - +
395E SER* 3.2 16.7 + - - +
396E ASP* 1.3 88.4 - - + +
398E VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 398 (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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320E ILE 3.7 1.0 - - - +
321E LYS* 3.4 5.7 - - - +
322E LEU* 2.9 42.0 + - + +
324E LYS* 4.7 1.1 - - - -
329E LEU* 3.9 33.9 - - + -
374E VAL* 3.8 25.8 - - + -
375E ASN* 3.8 2.2 - - - -
394E THR* 3.7 17.0 - - - +
395E SER 3.7 14.4 - - - +
396E ASP 4.2 3.6 - - - +
397E PHE* 1.3 80.2 - - - +
399E TYR* 1.3 61.8 + - - +
400E LEU* 4.0 20.6 - - + -
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Residues in contact with TYR 399 (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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319E GLU* 2.6 52.6 + - + +
320E ILE 3.8 2.2 - - - -
321E LYS* 4.6 23.1 - - + +
374E VAL* 3.3 5.4 - - - -
375E ASN* 2.7 45.7 + - - +
376E ASN* 3.7 40.6 + - - -
398E VAL* 1.3 74.9 - - - +
400E LEU* 1.3 59.5 + - - +
401E LYS* 4.4 27.2 - - + +
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Residues in contact with LEU 400 (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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319E GLU* 3.5 4.7 - - - +
320E ILE* 2.8 49.9 + - + +
322E LEU* 4.1 20.6 - - + -
331E PHE* 4.0 26.5 - - + -
365E LEU* 4.6 17.7 - - + -
371E LEU* 4.6 13.0 - - + -
373E ALA 3.5 11.0 - - - +
374E VAL* 4.0 19.7 - - + -
391E LEU* 4.1 17.3 - - + -
398E VAL* 4.0 12.1 - - + -
399E TYR* 1.3 75.5 - - - +
401E LYS* 1.3 60.1 + - - +
402E VAL* 3.9 11.2 + - + -
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Residues in contact with LYS 401 (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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317E ILE* 3.8 39.0 - - + +
318E MET 3.9 3.4 - - - +
319E GLU* 4.9 4.0 - - + +
371E LEU* 3.6 1.0 - - - +
372E LEU* 2.7 45.0 + - + -
373E ALA* 2.9 34.0 + - + +
376E ASN* 4.8 9.6 + - - +
399E TYR* 4.1 21.0 + - + +
400E LEU* 1.3 71.7 - - - +
402E VAL* 1.3 57.0 + - - +
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Residues in contact with VAL 402 (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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316E LYS 3.7 0.2 - - - +
317E ILE* 3.3 6.2 - - - +
318E MET* 3.1 58.1 + - + +
320E ILE* 3.7 18.4 - - + -
365E LEU* 3.9 23.1 - - + -
369E ASP* 4.4 15.9 - - + +
370E LYS 3.2 8.7 - - - +
371E LEU* 3.9 15.3 - - + -
372E LEU* 3.8 4.9 - - - +
400E LEU* 4.2 11.7 - - + -
401E LYS* 1.3 80.6 - - - +
403E ALA* 1.3 64.0 + - - +
404E LYS* 4.8 2.0 - - + -
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Residues in contact with ALA 403 (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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316E LYS* 3.5 18.6 - - + +
317E ILE* 4.9 1.3 - - + -
369E ASP* 3.8 3.3 - - - +
370E LYS* 2.8 48.2 + - + +
372E LEU* 3.8 21.9 - - + +
402E VAL* 1.3 74.3 - - - +
404E LYS* 1.3 61.9 + - - +
405E PRO* 3.7 4.5 - - - +
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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