Contacts of the strand formed by residues 396 - 400 (chain D) in PDB entry 1YKN
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 LEU 396 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ILE* 4.2 11.9 - - + -
94C ARG* 4.9 2.7 - - - +
351D PHE* 3.6 46.3 - - + -
354D LEU* 5.1 4.9 - - + -
356D PHE* 4.0 31.0 - - + -
395D THR* 1.3 76.4 - - - +
397D VAL* 1.3 62.3 + - - +
398D GLU* 3.7 37.2 - - + +
428D ARG* 4.3 6.5 - - + +
429D CME 4.0 5.6 - - - +
430D LEU* 4.0 4.0 - - + -
464D GLY 3.5 1.6 - - - +
465D ILE* 3.3 6.6 - - - +
466D SER* 3.1 33.5 + - - +
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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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384D VAL* 4.5 8.7 - - + -
395D THR* 4.2 3.1 - - + +
396D LEU* 1.3 74.6 - - - +
398D GLU* 1.3 63.1 + - - +
428D ARG* 3.3 3.6 - - - +
429D CME 3.0 36.8 + - + +
431D THR* 3.8 28.9 - - + -
437D TYR* 4.3 15.0 - - + -
439D PHE* 3.7 16.8 - - + -
463D PHE* 3.7 34.8 - - + -
464D GLY 3.4 5.2 - - - +
465D ILE* 4.7 7.6 - - + -
525D ILE* 5.2 0.7 - - + -
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Residues in contact with GLU 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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20C GLY 4.4 6.6 - - - +
21C LEU* 3.4 21.4 - - + +
31C ARG* 5.1 7.5 + - - +
35C ILE* 4.8 1.9 - - - +
94C ARG* 2.8 43.0 + - - -
396D LEU* 3.7 26.3 - - + +
397D VAL* 1.3 78.9 - - - +
399D MET* 1.3 64.0 + - - +
400D TRP* 4.3 2.9 - - + -
427D GLY 3.5 6.3 - - - +
428D ARG* 4.1 16.7 + - + +
463D PHE* 3.3 4.0 - - - +
464D GLY 2.8 41.6 + - - +
473D LYS* 5.0 2.4 + - - -
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Residues in contact with MET 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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20C GLY* 5.0 0.2 - - - -
363D LEU* 3.9 31.2 - - + -
380D VAL* 5.2 1.8 - - + -
398D GLU* 1.3 79.0 - - - +
400D TRP* 1.3 72.5 + - - +
401D GLN* 4.0 17.5 - - - +
426D VAL* 3.4 4.2 - - - +
427D GLY 2.9 39.9 + - - +
439D PHE* 3.7 49.8 - - + -
441D THR* 4.4 6.7 - - + -
461D ILE* 4.1 23.1 - - + -
462D HIS 3.2 12.8 - - - +
463D PHE* 4.5 9.2 - - + -
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Residues in contact with TRP 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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13C ALA 4.0 9.8 + - - -
16C TYR* 3.7 25.4 + - + +
17C VAL* 4.0 22.3 - - + +
19C ILE* 3.8 12.6 - - + -
20C GLY* 3.6 29.6 - - - +
21C LEU* 3.9 33.0 - - + -
398D GLU 4.3 9.2 - - - -
399D MET* 1.3 86.7 - - - +
401D GLN* 1.3 66.6 + - - +
408D GLU* 5.5 3.1 - - - -
425D GLY 2.9 13.7 - - - +
461D ILE* 3.6 1.8 - - - +
462D HIS* 2.9 74.7 + + + -
463D PHE 4.6 1.1 - - - -
464D GLY* 4.3 7.2 - - - -
475D ILE* 4.3 19.3 - - + -
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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