Contacts of the strand formed by residues 129 - 134 (chain A) 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 SER 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A CYS* 3.3 3.0 - - - +
108A ALA* 2.7 39.3 + - - +
111A GLN* 3.4 31.9 + - - -
128A GLY* 1.3 75.8 - - - -
130A CYS* 1.3 64.6 + - - +
131A PHE* 4.2 4.6 - - - -
142A GLU* 3.7 21.0 + - - +
143A TYR 4.0 1.8 - - - -
144A SER* 3.5 20.5 + - - +
169A ALA* 3.7 6.6 + - - -
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Residues in contact with CYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 4.2 11.4 - - + -
106A ALA 3.3 3.1 - - - +
107A CYS* 2.1 45.3 - - - -
129A SER* 1.3 75.0 + - - +
131A PHE* 1.3 62.9 + - - +
132A LEU* 3.7 7.0 - - + +
142A GLU* 3.4 6.4 - - - +
143A TYR* 2.9 39.9 + - + +
169A ALA 4.8 0.4 - - - -
170A GLY* 3.6 5.6 - - - -
181A LEU* 5.0 1.1 - - + -
183A LEU* 3.6 36.1 - - + -
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 3.7 36.8 - + + -
71A ASP* 4.2 13.7 - - + -
88A LYS* 4.1 19.3 - - - -
91A GLN* 4.1 11.7 - - - -
93A LEU* 3.4 31.0 - - + -
104A ILE 4.0 0.5 - - - +
105A VAL* 3.5 2.5 - - - -
106A ALA 2.6 35.7 + - - +
108A ALA* 4.2 7.2 - - + -
111A GLN* 3.7 26.2 - - - -
129A SER* 4.2 8.1 - - - -
130A CYS* 1.3 74.6 - - - +
132A LEU* 1.3 63.0 + - - +
133A ALA 4.1 0.2 + - - -
141A ALA 3.7 5.4 - - - +
142A GLU* 3.2 33.9 - - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.4 0.7 - - - -
103A VAL* 4.4 7.4 - - + -
104A ILE 3.6 2.0 - - - -
105A VAL* 3.2 39.3 - - + -
130A CYS* 3.7 17.9 - - + +
131A PHE* 1.3 76.9 - - - +
133A ALA* 1.3 62.6 + - - +
140A ARG* 3.3 7.4 - - - +
141A ALA* 2.9 38.9 + - + +
143A TYR* 4.1 10.8 - - + +
181A LEU* 4.3 11.2 - - + -
200A VAL* 4.6 9.6 - - + -
203A ILE* 4.0 28.0 - - + -
204A PHE* 3.6 24.2 - - + -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.5 10.8 - - + -
70A PHE* 3.7 28.5 - - + -
103A VAL* 3.3 6.6 - - - +
104A ILE* 2.8 40.7 + - + +
132A LEU* 1.3 76.7 - - - +
134A GLN* 1.3 59.5 + - - +
135A PRO* 3.4 4.7 - - + +
139A ARG 3.6 4.5 - - - -
140A ARG* 3.7 19.1 - - - +
204A PHE* 4.1 2.9 - - - -
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Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 5.9 0.4 - - - -
102A ASP* 2.9 41.7 + - - +
103A VAL* 4.6 5.1 - - + +
133A ALA* 1.3 72.6 - - - +
135A PRO* 1.3 53.5 - - - +
136A GLU* 2.9 20.2 + - + +
137A SER* 3.1 27.9 + - - +
138A GLY* 2.9 20.4 + - - -
139A ARG* 3.2 45.4 + - + +
140A ARG* 4.8 0.2 - - - -
204A PHE* 4.5 9.6 - - + -
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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