Contacts of the strand formed by residues 107 - 115 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E ASP* 2.8 44.1 + - + -
26E LEU 3.4 8.1 - - - +
27E ARG* 3.4 46.5 - - + +
61E ARG* 3.0 58.4 + - - +
64E THR* 4.6 1.0 + - - -
68E PHE* 4.6 6.6 - - - -
105E GLY 3.3 0.4 + - - -
106E ASP* 1.3 69.5 - - - +
108E ILE* 1.3 59.6 - - - +
109E CYS 3.7 0.9 - - - -
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Residues in contact with ILE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU 3.1 3.9 + - - +
28E ALA* 4.5 3.6 - - + +
42E VAL* 3.7 26.2 - - + -
44E LEU* 3.8 22.0 - - + -
60E PRO* 4.0 2.1 - - - +
61E ARG* 3.5 6.0 + - - -
64E THR* 2.7 33.9 + - + +
68E PHE* 3.8 28.7 - - + -
92E PHE* 3.7 30.8 - - + -
102E ILE* 3.9 26.0 - - + -
106E ASP* 3.1 15.8 + - + +
107E ARG* 1.3 73.7 - - - +
109E CYS* 1.3 67.0 + - - +
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Residues in contact with CYS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ASP* 3.4 7.1 - - - +
26E LEU* 2.9 34.5 + - - +
44E LEU* 3.6 36.3 - - - -
58E VAL* 3.7 17.0 - - + -
59E VAL 3.3 15.7 - - - +
61E ARG* 3.9 7.4 - - - +
92E PHE* 3.5 24.7 - - + -
107E ARG 3.7 0.2 - - - -
108E ILE* 1.3 83.1 - - - +
110E GLN* 1.3 63.5 + - - +
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Residues in contact with GLN 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E TRP* 3.4 40.5 - - + +
24E ILE 3.2 9.6 - - - +
25E ASP* 3.6 16.7 - - - +
26E LEU* 4.5 1.6 - - - +
58E VAL* 3.4 4.5 - - - -
59E VAL* 2.9 43.3 + - + +
60E PRO 4.0 9.6 - - - +
61E ARG* 3.8 17.1 - - + +
62E SER 4.8 2.0 + - - -
109E CYS* 1.3 78.4 - - - +
111E PHE* 1.3 61.0 + - - +
143E DUD 5.0 5.7 + - - -
78F VAL* 3.9 21.6 - - - +
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Residues in contact with PHE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ILE* 4.4 10.8 - - + -
5E ILE* 6.1 0.2 - - + -
15E ILE* 5.3 1.1 - - + -
23E TRP* 3.4 10.7 - - - -
24E ILE* 2.8 85.4 + - + +
26E LEU* 3.7 21.8 - - + -
48E MET* 3.8 30.1 - - + -
50E LEU* 4.9 0.7 - - + -
56E ALA* 4.1 2.5 - - + -
57E HIS 3.0 13.2 - - - +
58E VAL* 4.0 15.0 - - + -
90E TRP* 3.9 20.4 - + + -
110E GLN* 1.3 74.1 - - - +
112E ARG* 1.3 73.8 + - - +
113E ILE* 4.3 17.0 - - + -
117F MET* 3.9 2.2 - - - +
122F LEU* 5.0 5.6 - - + -
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Residues in contact with ARG 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLY 5.7 0.2 - - - +
23E TRP* 3.4 43.7 - - + +
56E ALA* 3.2 5.2 - - - +
57E HIS* 2.8 37.9 + - + +
111E PHE* 1.3 79.2 - - - +
113E ILE* 1.3 83.5 + - - +
114E MET* 4.0 28.4 - - - +
55F GLU* 2.8 29.6 + - - +
57F HIS* 5.1 0.2 - - - -
114F MET* 4.2 11.5 - - - +
115F LYS 2.9 24.7 + - - -
116F LYS* 3.6 2.2 + - - +
117F MET* 3.3 49.1 - - + +
118F PRO* 4.9 1.4 - - - +
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Residues in contact with ILE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 4.1 20.9 - - - -
3E ILE* 4.2 12.6 - - + -
50E LEU* 4.0 26.5 - - + -
51E PRO* 4.3 9.4 - - + -
54E TYR* 3.8 24.2 - - + -
55E GLU 3.1 12.3 - - - +
56E ALA* 4.5 0.9 - - - -
111E PHE* 4.3 7.2 - - + -
112E ARG* 1.3 102.1 + - - +
114E MET* 1.3 59.6 + - - +
117F MET* 3.4 23.1 - - + +
118F PRO* 4.5 7.2 - - + +
120F VAL* 4.1 21.8 - - + -
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Residues in contact with MET 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ARG* 4.0 11.4 - - - +
114D MET* 3.7 28.0 - - + +
54E TYR* 3.3 8.3 - - - -
55E GLU* 2.8 32.0 + - - +
57E HIS* 3.7 34.9 + - + +
112E ARG* 4.0 26.9 - - - +
113E ILE* 1.3 73.4 - - - +
115E LYS* 1.3 70.6 + - + +
57F HIS* 5.0 2.9 - - + -
114F MET* 3.2 33.9 - - + +
118F PRO* 6.1 0.2 - - - -
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Residues in contact with LYS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ARG* 2.9 23.9 + - - -
52E GLU 5.2 1.1 - - - -
53E GLY* 3.0 34.2 + - - -
54E TYR* 3.4 43.2 - - + +
114E MET* 1.3 80.3 - - + +
116E LYS* 1.3 74.0 + - - +
117E MET 5.6 0.4 + - - -
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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