Contacts of the strand formed by residues 59 - 64 (chain D) in PDB entry 6D6U
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 GLU 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PRO 4.3 0.9 - - - +
53D VAL* 4.4 1.1 - - - +
54D SER* 3.0 31.9 + - - +
57D ASP* 4.2 20.6 - - + +
58D MET* 1.3 79.3 - - - +
60D TYR* 1.3 63.7 + - - +
61D THR* 5.4 2.3 + - - +
105D LYS* 3.2 31.5 + - - +
136D ARG* 3.3 34.6 + - + +
137D ALA 3.3 17.7 - - - +
138D GLU* 4.6 0.4 - - - +
139D CYS* 5.4 0.4 - - - -
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Residues in contact with TYR 60 (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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50D PHE* 3.7 33.7 - + - -
52D PRO 4.3 4.3 - - - -
53D VAL* 3.7 27.8 - - + -
59D GLU* 1.3 76.8 - - - +
61D THR* 1.3 65.0 + - - +
62D ILE* 3.8 17.7 + - + +
136D ARG* 4.7 1.8 - - - -
137D ALA* 3.3 46.1 + - + +
138D GLU 4.4 0.4 - - - -
139D CYS* 3.7 24.7 - - + -
153D CYS* 3.7 17.3 + - + -
154D PRO 2.4 34.9 + - - -
155D LEU* 3.4 14.0 - - - +
217D PHE* 4.4 3.8 - + - -
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PHE* 4.4 1.6 - - - -
51D GLY* 2.7 35.1 + - - +
52D PRO* 4.0 27.7 + - + +
59D GLU* 5.4 2.9 + - - +
60D TYR* 1.3 77.3 - - - +
62D ILE* 1.3 61.3 + - - +
134D THR* 4.1 21.3 - - + -
135D VAL 3.5 11.9 - - - +
136D ARG* 3.9 24.9 + - - +
187D ARG* 4.9 9.6 - - - +
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Residues in contact with ILE 62 (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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47D VAL* 3.8 20.2 - - + -
49D SER 4.1 3.8 - - - +
50D PHE* 4.0 15.7 - - + -
51D GLY 4.3 0.4 - - - +
60D TYR* 4.2 18.2 - - + +
61D THR* 1.3 79.1 - - - +
63D ASP* 1.3 68.8 + - - +
64D VAL* 4.1 8.5 - - + -
134D THR* 3.5 3.4 - - - +
135D VAL* 2.8 63.8 + - + +
137D ALA 5.5 0.2 - - - +
155D LEU* 4.7 9.0 - - + -
187D ARG* 6.3 0.2 - - - -
217D PHE* 3.6 37.5 - - + -
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Residues in contact with ASP 63 (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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99C LEU 4.8 4.9 - - - +
47D VAL* 3.2 26.2 - - - +
48D THR* 3.2 23.8 + - - +
49D SER* 3.2 31.3 + - - +
62D ILE* 1.3 72.5 - - - +
64D VAL* 1.3 89.2 + - - +
65D PHE* 5.1 0.2 - - - -
110D HIS* 5.5 0.2 + - - -
132D ARG* 4.1 22.3 + - - +
133D LEU 2.8 19.2 - - - +
134D THR* 4.7 8.7 - - + +
187D ARG* 5.3 5.4 + - - +
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Residues in contact with VAL 64 (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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45D ILE* 3.7 30.7 - - + -
46D PHE 4.0 5.8 - - - -
47D VAL* 4.1 6.7 - - + -
62D ILE* 4.1 17.5 - - + -
63D ASP* 1.3 93.6 + - - +
65D PHE* 1.3 67.0 + - - +
66D PHE* 4.2 17.7 - - + +
101D PHE* 5.4 1.8 - - + -
132D ARG* 3.6 4.0 - - - -
133D LEU* 3.4 41.4 + - + -
135D VAL* 3.9 12.8 - - + -
155D LEU* 5.4 4.5 - - + -
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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