Contacts of the strand formed by residues 87 - 92 (chain D) in PDB entry 1TYE
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 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D LEU* 3.2 36.1 + - + +
65D GLU* 3.1 41.9 + - + +
85D PRO* 3.3 0.8 - - - +
86D GLN* 1.3 83.6 + - - +
88D ILE* 1.3 67.4 + - - +
425D LEU* 4.0 0.9 - - - -
426D ILE* 3.2 43.6 - - + +
428D GLN* 3.5 40.5 - - - +
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Residues in contact with ILE 88 (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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61D ALA* 5.4 5.8 - - + -
62D ARG 3.4 17.9 - - - +
63D VAL* 3.5 19.5 - - + -
64D LEU* 4.3 6.1 - - - +
85D PRO* 3.9 19.5 - - + -
87D ARG* 1.3 78.6 - - - +
89D ALA* 1.3 62.2 + - - +
90D LEU* 3.8 1.3 + - + +
100D PHE* 3.5 49.6 - - + -
101D SER 5.8 0.7 - - - +
425D LEU* 3.9 17.9 - - + -
426D ILE 2.9 10.6 + - - +
427D VAL* 3.5 12.3 - - + -
428D GLN* 2.8 28.9 + - - +
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Residues in contact with ALA 89 (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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60D GLU* 5.2 0.5 - - - +
61D ALA* 2.9 4.4 + - - -
62D ARG* 2.8 40.0 + - + +
64D LEU* 3.6 23.8 - - + +
88D ILE* 1.3 71.8 - - - +
90D LEU* 1.3 61.6 + - - +
91D ARG* 3.7 6.5 + - + +
428D GLN* 3.6 13.2 - - + +
430D THR* 5.5 4.3 - - - +
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Residues in contact with LEU 90 (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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61D ALA* 3.3 26.0 - - + +
88D ILE* 3.8 1.7 + - + -
89D ALA* 1.3 72.0 - - - +
91D ARG* 1.3 59.7 + - - +
92D LEU* 4.1 15.4 + - + +
98D LYS* 3.9 20.0 - - + -
100D PHE* 4.3 17.0 - - + -
366D LEU* 4.8 0.9 - - + -
401D ALA* 3.7 27.4 - - + -
414D PHE* 4.8 2.0 - - + -
427D VAL* 3.7 24.9 - - + -
428D GLN 2.8 11.2 + - - +
429D VAL* 3.2 24.2 - - + +
430D THR 2.8 25.2 + - - +
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Residues in contact with ARG 91 (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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58D VAL 5.6 0.9 - - - +
59D SER* 3.2 2.7 - - - -
60D GLU* 2.9 59.5 + - + +
61D ALA 3.9 4.7 + - - +
89D ALA* 3.7 10.3 + - + +
90D LEU* 1.3 73.8 - - - +
92D LEU* 1.3 64.0 + - - +
98D LYS* 5.3 0.5 - - - +
410D LYS* 4.8 4.4 - - - +
430D THR* 3.2 39.3 + - - +
431D PHE 4.2 5.3 + - - -
432D ASP* 3.2 46.5 + - + +
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Residues in contact with LEU 92 (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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59D SER* 3.1 21.3 - - - +
90D LEU* 4.2 29.4 - - + +
91D ARG* 1.3 77.4 - - - +
93D ARG* 1.3 63.5 + - - +
96D ASP* 4.4 2.9 - - + +
97D SER* 4.3 8.1 - - - -
98D LYS* 4.4 5.4 - - + +
366D LEU* 5.8 0.4 - - + -
401D ALA* 3.8 20.2 - - + +
403D VAL* 3.3 36.7 - - + +
406D CYS* 5.0 0.7 - - - -
429D VAL* 5.4 1.3 - - + -
430D THR 3.1 7.1 + - - +
431D PHE* 3.7 26.9 - - + +
432D ASP* 3.4 19.5 + - - +
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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