Contacts of the strand formed by residues 107 - 115 (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 ARG 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D ASP* 2.8 45.2 + - + -
26D LEU 3.4 6.7 - - - +
27D ARG* 3.6 45.6 - - + +
61D ARG* 3.1 60.3 + - - +
64D THR* 4.6 0.9 + - - -
68D PHE* 4.2 8.5 - - - -
105D GLY 3.3 0.4 + - - -
106D ASP* 1.3 67.6 - - - +
108D ILE* 1.3 62.9 + - - +
109D CYS 3.7 1.1 - - - -
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Residues in contact with ILE 108 (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 3.1 3.9 + - - +
28D ALA* 4.3 5.2 - - + +
42D VAL* 3.4 35.2 - - + -
44D LEU* 3.9 18.4 - - + -
60D PRO* 4.0 1.7 - - - +
61D ARG* 3.6 3.9 + - - -
64D THR* 2.6 34.9 + - + +
68D PHE* 3.7 27.6 - - + -
70D VAL* 6.2 0.4 - - + -
92D PHE* 3.8 30.1 - - + -
102D ILE* 3.8 25.6 - - + -
106D ASP* 3.2 13.4 + - + +
107D ARG* 1.3 74.8 - - - +
109D CYS* 1.3 64.6 + - - +
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Residues in contact with CYS 109 (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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25D ASP* 3.4 5.7 - - - +
26D LEU* 2.8 34.6 + - - +
44D LEU* 3.7 40.2 - - - -
58D VAL* 3.8 15.7 - - + -
59D VAL 3.3 15.3 - - - +
61D ARG* 3.9 10.2 - - - +
92D PHE* 3.6 23.1 - - + -
107D ARG 3.7 0.6 - - - -
108D ILE* 1.3 79.7 - - - +
110D GLN* 1.3 60.3 + - - +
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Residues in contact with GLN 110 (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* 3.4 39.5 - - + +
24D ILE 3.2 10.1 - - - +
25D ASP* 3.5 17.2 - - - +
26D LEU* 4.5 1.3 - - - +
57D HIS 3.6 0.2 - - - +
58D VAL* 3.3 5.3 - - - +
59D VAL* 2.9 44.2 + - + +
60D PRO 3.9 9.9 - - - +
61D ARG* 3.7 19.0 + - + +
62D SER 4.7 1.9 + - - -
109D CYS* 1.3 77.2 - - - +
111D PHE* 1.4 60.6 - - - +
78E VAL* 4.1 20.0 + - - +
144E DUD 4.9 10.1 + - - -
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Residues in contact with PHE 111 (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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3D ILE* 4.4 9.6 - - + -
5D ILE* 6.1 0.2 - - + -
15D ILE* 5.2 1.8 - - + -
23D TRP* 3.4 9.2 - - - -
24D ILE* 2.8 90.0 + - + +
26D LEU* 3.9 27.4 - - + -
48D MET* 3.8 24.0 - - + -
50D LEU* 4.7 0.4 - - + -
56D ALA* 3.9 2.9 - - + -
57D HIS 3.0 18.4 - - - +
58D VAL* 4.1 12.1 - - + -
90D TRP* 3.9 20.4 - + + -
110D GLN* 1.4 74.4 - - - +
112D ARG* 1.3 72.4 + - - +
113D ILE* 4.3 17.9 - - + -
117E MET* 4.1 1.4 - - - +
122E LEU* 5.5 3.6 - - + -
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Residues in contact with ARG 112 (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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21D GLY 5.7 0.2 - - - +
23D TRP* 3.4 44.8 - - + +
56D ALA* 3.3 2.4 - - - +
57D HIS* 3.0 32.0 + - + -
111D PHE* 1.3 80.8 - - - +
113D ILE* 1.3 85.6 + - - +
114D MET* 4.0 26.7 - - + +
55E GLU* 3.0 19.7 + - - -
57E HIS* 5.1 0.7 - - - -
114E MET* 4.0 12.5 - - - -
115E LYS 2.9 26.3 + - - -
116E LYS 3.8 1.0 + - - -
117E MET* 3.4 48.0 - - + +
118E PRO* 4.9 1.8 - - - +
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Residues in contact with ILE 113 (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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1D MET* 4.3 9.6 - - - -
3D ILE* 4.0 12.6 - - + -
50D LEU* 4.0 27.4 - - + -
51D PRO* 4.0 24.0 - - + -
54D TYR* 3.8 27.8 - - + -
55D GLU 3.1 12.6 - - - +
56D ALA* 4.6 1.3 - - + -
111D PHE* 4.3 5.8 - - + -
112D ARG* 1.3 100.5 + - - +
114D MET* 1.3 61.9 - - - +
117E MET* 3.5 20.8 - - + +
118E PRO* 4.5 5.6 - - + +
120E VAL* 4.5 19.1 - - + -
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Residues in contact with MET 114 (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* 6.0 0.4 - - + -
54D TYR* 3.3 7.4 - - - -
55D GLU* 2.8 31.8 + - + +
57D HIS* 3.4 42.4 - - + +
112D ARG* 4.0 24.2 - - - +
113D ILE* 1.3 75.6 - - - +
115D LYS* 1.3 76.1 + - + +
57E HIS* 5.0 4.7 - - + -
114E MET* 3.7 26.5 - - + +
112F ARG* 4.1 7.9 - - - +
114F MET* 3.8 28.9 - - + +
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Residues in contact with LYS 115 (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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52D GLU 5.5 0.4 + - - -
53D GLY* 3.8 17.5 + - - -
54D TYR* 3.4 41.5 - - + +
114D MET* 1.3 79.5 - - - +
116D LYS* 1.3 69.1 + - - +
112F ARG* 2.9 23.8 + - - -
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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