Contacts of the strand formed by residues 54 - 60 (chain D) in PDB entry 2Y1T
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 TYR 54 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 4.0 27.4 - - + +
50D LEU* 4.3 4.9 - - + +
51D PRO* 3.1 29.6 + - + +
52D GLU 3.3 23.3 - - - -
53D GLY* 1.3 82.2 - - - +
55D GLU* 1.3 63.0 + - - +
81D GLU* 3.3 28.8 + - - +
113D ILE* 3.8 28.5 - - + -
114D MET* 3.3 22.9 - - - -
115D LYS* 3.4 40.6 - - + +
116D LYS* 3.9 4.8 - - - +
118E PRO* 4.2 15.3 - - + +
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Residues in contact with GLU 55 (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 LEU* 3.8 5.4 - - - -
54D TYR* 1.3 76.2 - - - +
56D ALA* 1.3 57.8 + - - +
57D HIS* 2.8 32.1 + - + +
78D VAL* 4.0 6.1 - - + +
79D ILE 3.2 15.7 - - - +
80D ASP* 4.4 6.1 - - - +
113D ILE* 3.1 5.6 - - - +
114D MET* 2.8 40.3 + - - +
116D LYS* 3.5 20.9 - - + +
21F GLY 4.5 1.7 - - - +
22F ASP* 5.7 0.2 - - - -
23F TRP* 2.9 36.5 + - - -
112F ARG* 2.9 22.5 + - - +
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Residues in contact with ALA 56 (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 LEU* 3.4 13.3 - - + +
55D GLU* 1.3 71.5 - - - +
57D HIS* 1.3 72.6 + - - +
58D VAL 4.2 0.2 - - - -
77D GLY 3.5 0.3 - - - +
78D VAL* 3.3 3.6 - - - +
79D ILE* 2.8 42.5 + - + +
90D TRP* 3.6 32.1 - - + -
111D PHE* 3.9 10.5 - - + -
112D ARG 3.3 9.9 - - - +
113D ILE* 4.2 1.1 - - + +
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Residues in contact with HIS 57 (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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23D TRP* 3.5 17.0 - - + -
55D GLU* 2.8 36.8 + - + +
56D ALA* 1.3 83.8 - - - +
58D VAL* 1.3 64.1 + - - +
59D VAL 4.2 0.2 - - - -
76D MET* 3.5 39.2 - - + -
77D GLY 3.4 2.7 - - - -
78D VAL* 4.4 5.8 - - + -
111D PHE* 3.0 25.3 - - - -
112D ARG* 3.0 14.0 + - + +
114D MET* 3.4 40.4 - - + +
76E MET* 5.7 1.6 - - - +
23F TRP* 4.0 9.3 - + - -
57F HIS* 6.1 0.2 - - - -
112F ARG* 4.8 0.9 - - - -
114F MET* 5.0 5.4 - - + -
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Residues in contact with VAL 58 (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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26D LEU* 5.0 1.8 - - + -
44D LEU* 5.2 4.0 - - + -
57D HIS* 1.3 79.9 - - - +
59D VAL* 1.3 62.7 + - - +
72D GLN* 3.2 11.9 + - - +
76D MET* 3.2 8.2 - - - +
77D GLY* 2.9 38.6 + - - +
79D ILE* 4.1 18.8 - - + -
90D TRP* 3.9 31.4 - - + -
91D PHE 5.4 3.1 - - - +
92D PHE* 4.9 2.0 - - + -
93D PRO* 6.3 0.2 - - + -
109D CYS* 3.8 31.2 - - + -
110D GLN 3.3 6.3 - - - +
111D PHE* 4.1 3.8 - - + -
143D DUD 5.0 5.8 - - + +
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Residues in contact with VAL 59 (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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23D TRP* 3.5 28.5 - - + -
58D VAL* 1.3 79.9 - - - +
60D PRO* 1.3 85.6 - - + +
72D GLN* 3.3 6.1 - - - -
75D SER 4.2 3.4 - - - +
76D MET* 3.8 31.6 - - + -
109D CYS* 3.3 3.8 - - - +
110D GLN* 2.9 38.0 + - + +
74E ASN 4.3 3.6 - - - +
76E MET* 4.1 29.2 - - + +
78E VAL* 4.9 2.2 - - + -
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Residues in contact with PRO 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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59D VAL* 1.3 95.4 - - + +
61D ARG* 1.3 70.5 + - - +
62D SER 3.7 0.5 + - - -
64D THR* 4.0 15.5 - - + -
70D VAL 5.5 0.7 - - - +
71D ILE* 5.2 0.9 - - - -
72D GLN* 3.1 33.1 - - + +
75D SER 4.2 0.2 - - - +
92D PHE* 4.0 7.0 - - + -
108D ILE 4.0 7.4 - - - +
109D CYS* 4.2 2.0 - - + -
110D GLN* 3.9 4.3 - - - +
73E THR 4.3 6.3 - - - +
74E ASN* 3.3 41.6 + - - +
75E SER* 3.7 10.8 - - - +
76E MET 4.8 1.6 - - - +
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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