Contacts of the strand formed by residues 414 - 418 (chain D) in PDB entry 1Y8Q
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 414 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334C MET 3.3 22.4 + - - -
335C LYS* 3.3 51.5 + - - +
148D VAL 3.8 4.7 - - - +
149D THR* 4.2 5.9 - - - -
150D THR 4.8 0.9 + - - -
401D GLU* 3.0 25.0 + - - +
404D LYS* 4.6 1.7 - - - +
412D GLN* 3.0 27.7 + - - +
413D CYS* 1.3 78.1 - - - +
415D THR* 1.3 60.2 + - - +
416D ILE* 3.5 9.7 + - + +
431D PRO* 4.0 16.9 - - + +
432D CYS 2.8 28.9 - - - +
433D ALA* 4.6 2.2 - - - +
434D LEU* 3.8 12.7 - - - +
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Residues in contact with THR 415 (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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147D GLN* 4.7 6.3 - - - +
148D VAL 3.2 11.9 - - - +
149D THR* 2.8 23.9 + - - -
414D ARG* 1.3 70.7 - - - +
416D ILE* 1.3 62.5 + - - +
417D PHE* 3.4 34.1 - - + -
430D VAL 3.5 2.6 - - - +
431D PRO 3.6 0.2 - - - -
432D CYS* 2.7 45.6 + - - +
433D ALA 5.0 2.9 + - - -
434D LEU* 3.7 9.2 - - - +
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Residues in contact with ILE 416 (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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336C GLY* 4.0 35.2 - - - +
147D GLN* 3.2 7.3 - - - +
148D VAL* 3.0 35.1 + - + +
397D LEU* 3.9 43.1 - - + +
401D GLU* 4.0 23.3 - - + +
414D ARG* 4.0 11.7 - - + +
415D THR* 1.3 78.4 - - - +
417D PHE* 1.3 70.7 + - - +
418D LEU 4.2 0.2 + - - -
429D LEU* 4.1 8.3 - - + -
430D VAL 3.5 5.8 - - - +
431D PRO* 4.4 10.5 - - + -
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Residues in contact with PHE 417 (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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146D GLY 3.7 3.6 - - - -
147D GLN* 3.6 37.5 - - + -
415D THR* 3.4 24.9 - - + -
416D ILE* 1.3 77.4 - - - +
418D LEU* 1.3 60.7 + - - +
419D ASN* 3.9 12.3 - - - +
428D LEU 3.6 1.2 - - - +
429D LEU* 3.3 8.3 - - - +
430D VAL* 2.9 51.2 + - + +
432D CYS* 3.8 20.6 - - + -
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Residues in contact with LEU 418 (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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309C ILE* 4.4 17.5 - - + -
312C GLN* 5.6 6.5 - - - +
144D TYR 3.7 19.1 - - - +
145D LEU* 3.3 16.8 - - - +
146D GLY 2.9 28.4 + - - +
390D THR* 3.9 13.0 - - + -
393D VAL* 4.0 16.2 - - + -
394D ILE* 3.5 27.6 - - + -
397D LEU* 5.6 0.9 - - + -
416D ILE 4.2 0.4 + - - -
417D PHE* 1.3 72.4 - - - +
419D ASN* 1.3 71.0 + - - +
428D LEU* 4.3 6.3 - - + +
429D LEU* 3.5 28.0 - - + -
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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