Contacts of the strand formed by residues 112 - 117 (chain E) 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 HIS 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E THR* 3.3 6.1 - - - -
87E PHE* 2.7 53.4 + - + +
89E ALA 5.0 5.3 + - - -
90E ARG* 6.6 0.4 - - + -
110E TRP* 3.1 29.4 + - + -
111E GLN* 1.3 76.9 - - - +
113E TRP* 1.3 60.1 + - - +
124E LYS* 3.9 18.8 - - + -
125E THR* 3.2 28.7 - - - -
126E PRO* 3.3 15.5 - - + +
127E VAL* 5.3 0.4 - - - -
162F SER* 3.0 33.6 + - - -
167F ILE* 3.9 12.3 - - + +
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Residues in contact with TRP 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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84E LEU* 3.8 22.4 - - + -
85E GLN 3.1 32.1 - - - -
86E THR* 3.6 17.9 - - + -
87E PHE* 4.5 2.9 - - - -
111E GLN* 6.0 0.4 - - - +
112E HIS* 1.3 77.7 - - - +
114E ASN* 1.3 67.9 + - - +
115E VAL* 3.7 17.2 - - + +
122E ALA* 5.5 4.9 - - + +
123E GLU 2.9 17.5 - - - +
124E LYS* 3.3 1.1 - - - -
125E THR* 2.9 18.5 + - - +
127E VAL* 3.8 33.9 - - + -
147E ARG* 3.3 40.6 - - + +
148E GLY 2.9 37.2 + - - +
165E ARG* 6.3 2.0 - - + -
212E LEU* 3.8 21.3 - - + -
213E LEU* 4.3 7.0 - - + -
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Residues in contact with ASN 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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85E GLN* 2.9 54.9 + - + +
87E PHE* 4.2 5.2 - - + -
113E TRP* 1.3 81.8 - - - +
115E VAL* 1.3 86.6 + - - +
116E LEU* 3.9 8.7 - - - +
121E GLU* 3.3 21.2 + - - +
122E ALA* 3.4 5.0 + - - -
123E GLU 2.7 43.4 + - - +
124E LYS* 3.4 12.3 - - - +
168F SER* 4.1 2.6 + - - -
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Residues in contact with VAL 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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82E GLN* 3.8 41.1 - - + +
83E THR 3.2 4.0 - - - -
84E LEU* 4.0 11.9 - - + -
113E TRP* 3.7 14.1 - - + +
114E ASN* 1.3 88.4 + - - +
116E LEU* 1.3 62.2 + - - +
121E GLU* 3.1 6.6 - - - -
122E ALA* 2.9 36.4 + - + +
148E GLY 3.2 27.4 - - - +
149E ASN* 4.0 9.2 - - + +
151E LEU* 4.4 5.8 - - + +
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Residues in contact with LEU 116 (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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81E SER 3.8 0.9 - - - +
82E GLN* 3.1 7.3 - - - +
83E THR* 2.7 53.8 + - + +
85E GLN* 3.6 29.8 - - - +
114E ASN* 3.9 10.3 - - - +
115E VAL* 1.3 73.7 - - - +
117E GLU* 1.3 59.9 + - - +
118E LYS 4.1 5.2 - - - +
120E GLU 3.7 3.8 - - - +
121E GLU* 3.5 35.7 - - + +
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Residues in contact with GLU 117 (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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81E SER* 3.7 29.8 - - - +
82E GLN* 3.0 33.5 + - + -
115E VAL 4.2 0.2 + - - -
116E LEU* 1.3 74.5 - - - +
118E LYS* 1.3 79.8 + - + +
120E GLU* 3.0 26.3 + - - +
151E LEU* 3.7 36.0 - - + +
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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