Contacts of the strand formed by residues 395 - 401 (chain D) in PDB entry 1K8F
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 LYS 395 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375D CYS 3.0 5.9 + - - +
376D LYS* 3.3 29.8 - - + +
377D LYS 3.0 20.8 + - - -
393D ASN 4.9 3.0 + - - -
394D SER* 1.3 91.7 + - - +
396D ASP* 1.3 73.3 + - - +
397D VAL* 3.5 1.8 + - - +
412D LYS 4.3 9.5 + - - -
414D ASP* 3.3 37.0 + - + +
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Residues in contact with ASP 396 (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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377D LYS* 3.2 56.8 + - + +
378D LEU 3.3 2.8 + - - +
395D LYS* 1.3 79.7 - - - +
397D VAL* 1.3 59.8 + - - +
398D LYS 4.2 0.3 + - - -
414D ASP 3.0 16.4 + - - +
415D GLY* 3.0 15.2 + - - -
417D HIS* 6.0 2.5 - - - -
436D GLU* 5.1 4.0 - - - +
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Residues in contact with VAL 397 (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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372D VAL* 4.0 16.8 - - + -
375D CYS 4.3 3.1 - - - +
378D LEU* 3.4 20.9 - - + +
380D LEU* 5.7 0.2 - - + -
391D ILE* 3.9 22.4 - - + -
394D SER* 3.5 32.1 - - - -
395D LYS 4.1 4.9 - - - +
396D ASP* 1.3 78.8 - - - +
398D LYS* 1.3 64.3 + - - +
399D VAL* 3.8 22.4 - - + -
413D THR* 5.1 0.2 - - + -
415D GLY 2.9 8.6 + - - +
416D CYS* 3.2 8.3 - - - -
417D HIS* 3.0 26.4 + - - -
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Residues in contact with LYS 398 (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 2.9 12.2 + - - +
379D GLY* 4.4 8.0 - - - -
380D LEU* 2.7 58.7 + - - +
381D VAL* 4.6 8.9 - - - +
397D VAL* 1.3 73.7 - - - +
399D VAL* 1.3 57.1 + - - +
400D GLN* 4.3 16.5 + - - +
417D HIS* 3.6 9.4 - - + +
419D TYR* 3.5 40.6 - - + +
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Residues in contact with VAL 399 (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 LEU* 3.3 22.4 - - + -
382D PHE* 3.5 26.7 - - + -
389D VAL* 4.2 9.9 - - + -
391D ILE* 3.9 22.0 - - + -
397D VAL* 3.8 20.0 - - + -
398D LYS* 1.3 78.8 - - - +
400D GLN* 1.3 66.5 + - - +
401D VAL* 5.8 0.4 - - - -
408D ILE* 4.9 11.0 - - + -
416D CYS* 4.4 6.3 - - - -
417D HIS 3.0 11.2 + - - +
418D ALA* 3.6 5.3 - - - -
419D TYR* 2.8 29.7 + - - +
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Residues in contact with GLN 400 (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 LEU 2.9 12.4 + - - +
381D VAL* 4.2 11.5 - - + +
382D PHE* 2.9 33.5 + - - +
398D LYS* 4.3 15.4 + - - +
399D VAL* 1.3 77.4 - - - +
401D VAL* 1.3 70.0 + - - +
402D MET* 3.8 28.2 - - - +
419D TYR* 3.4 19.6 - - + +
420D LEU 4.6 1.8 + - - -
421D SER* 6.0 0.2 - - - -
448D PHE* 3.8 26.6 - - - -
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Residues in contact with VAL 401 (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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382D PHE* 3.3 34.1 - - + -
383D ASP 3.9 9.6 - - - +
400D GLN* 1.3 86.6 + - - +
402D MET* 1.3 61.3 + - - +
403D GLY 4.0 3.8 - - - +
404D LYS 3.9 9.4 - - - -
405D VAL* 3.5 30.3 - - + -
408D ILE* 4.6 5.4 - - + -
419D TYR 3.1 17.2 + - - +
420D LEU* 4.0 10.6 - - + +
421D SER* 3.3 16.8 - - - -
424D SER* 3.8 15.7 - - - +
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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