Contacts of the strand formed by residues 426 - 434 (chain D) in PDB entry 4JF7
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 GLN 426 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300D TRP* 4.1 14.1 - - + -
374D GLU* 5.1 5.0 - - - +
376D LEU* 3.7 29.8 - - + +
422D PHE* 3.6 4.6 - - - -
423D THR* 2.7 36.9 + - - +
424D ASN 4.5 5.8 - - - +
425D GLY* 1.3 85.5 - - - +
427D PRO* 1.3 69.1 - - + +
428D SER* 3.2 2.1 + - - -
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Residues in contact with PRO 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D TRP* 3.7 25.6 - - + -
302D LEU* 5.3 4.0 - - + -
364D ALA* 4.1 18.8 - - + -
376D LEU* 3.7 16.1 - - + +
378D LEU* 3.7 28.6 - - + +
420D ILE* 4.1 13.7 - - + -
421D THR 3.3 9.0 - - - +
422D PHE* 3.5 27.3 - - + -
426D GLN* 1.3 87.1 - - + +
428D SER* 1.3 58.8 + - - +
429D ALA 3.8 0.4 - - - -
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Residues in contact with SER 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D LEU* 3.6 13.4 - - - +
421D THR* 2.7 26.9 + - - -
423D THR* 2.9 37.5 + - - -
426D GLN* 3.2 1.5 + - - -
427D PRO* 1.3 74.6 - - - +
429D ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D LEU* 3.9 5.1 - - - +
419D THR 4.6 0.2 - - - -
420D ILE* 3.6 2.3 - - - +
421D THR* 3.0 43.0 + - + +
427D PRO 3.8 0.6 - - - -
428D SER* 1.3 84.1 + - - +
430D ILE* 1.3 71.1 + - - +
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Residues in contact with ILE 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D ILE* 4.2 13.9 - - + -
378D LEU* 3.1 48.2 - - + +
379D PRO 3.6 15.5 + - - +
380D PHE* 3.6 41.6 - - + +
381D SER* 5.0 5.5 + - - -
384D GLN* 4.4 3.3 + - - +
418D VAL* 4.2 10.3 - - + -
419D THR 3.5 3.6 - - - -
420D ILE* 4.1 21.5 - - + -
429D ALA* 1.3 82.3 - - - +
431D SER* 1.3 63.2 + - - +
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Residues in contact with SER 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D PHE* 4.8 0.9 - - - -
384D GLN* 3.5 19.7 + - - -
417D LYS 3.5 1.1 - - - +
418D VAL* 3.2 7.8 - - - +
419D THR* 2.8 47.2 + - - -
430D ILE* 1.3 77.7 - - - +
432D ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D PHE* 3.7 28.9 - - + -
384D GLN* 2.9 36.3 + - + +
385D VAL* 4.2 7.6 - - + -
416D TYR* 4.0 25.4 - - + -
417D LYS 3.5 3.8 - - - -
418D VAL* 4.7 0.4 - - + +
431D SER* 1.3 76.2 + - - +
433D GLN* 1.3 59.4 + - - +
434D ASN 4.1 1.3 + - - -
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Residues in contact with GLN 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416D TYR* 3.2 3.4 - - - +
417D LYS* 2.9 48.1 + - + +
432D ALA* 1.3 71.9 - - - +
434D ASN* 1.3 65.4 + - - +
478D PHE* 3.5 54.9 - - + +
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Residues in contact with ASN 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D PHE* 3.8 21.7 - - + -
326D PRO* 4.2 21.6 - - - +
327D GLN* 5.3 1.2 + - - +
384D GLN 5.1 0.4 + - - +
414D MET* 4.0 14.8 - - - +
415D LEU 2.9 29.2 + - - +
416D TYR* 3.6 26.0 - - + -
432D ALA 4.1 1.4 + - - -
433D GLN* 1.3 73.5 - - - +
435D VAL* 1.3 73.8 + - - +
436D PRO* 3.3 28.4 - - - +
478D PHE* 3.4 11.9 - - - -
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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