Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 1TA6
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 LYS 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER* 2.6 124.2 + - + +
133A GLY 4.1 3.6 - - - +
134A TYR* 1.3 74.2 - - - +
136A GLY* 1.3 60.2 + - - +
159A ASN* 4.9 2.7 - - + -
160A LEU 3.3 7.4 - - - +
161A PRO* 4.0 15.9 - - + -
184A TYR* 3.5 26.5 + - - +
186A LYS* 4.9 9.3 - - - +
201A MET* 3.5 5.1 - - - +
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Residues in contact with GLY 136 (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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14A LEU* 4.7 3.1 - - - -
134A TYR 4.0 0.2 + - - -
135A LYS* 1.3 74.4 - - - +
137A ARG* 1.3 61.2 + - - -
159A ASN* 3.2 7.2 - - - +
160A LEU 2.8 32.8 + - - -
199A PHE* 3.3 28.5 - - - -
200A VAL 3.3 11.2 - - - -
201A MET* 3.9 1.8 - - - -
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 3.9 1.8 - - - +
14A LEU* 2.8 85.9 + - + +
26A MET* 3.6 21.6 + - - +
27A SER* 5.1 4.5 - - - -
136A GLY* 1.3 73.9 - - - -
138A VAL* 1.3 69.0 + - - +
139A THR* 4.6 7.8 - - + +
157A VAL* 3.5 23.3 - - + +
158A VAL 3.4 3.6 - - - -
159A ASN* 3.1 20.3 + - - +
198A PRO 3.4 2.1 - - - +
199A PHE* 3.2 5.1 - - - -
200A VAL* 2.8 47.5 + - + +
207A TRP* 3.4 24.3 - - - -
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.9 16.8 - - + +
137A ARG* 1.3 74.2 - - - +
139A THR* 1.3 67.2 + - - +
157A VAL* 3.5 3.5 - - - +
158A VAL* 2.8 43.5 + - + +
160A LEU* 4.3 12.8 - - + -
190A ALA* 4.4 3.8 - - + -
194A ASP* 5.6 0.2 - - + -
198A PRO 3.6 5.8 - - - +
199A PHE* 3.5 33.4 - - + -
213A VAL* 3.5 31.0 - - + -
228A TYR* 3.5 18.6 - - + +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.1 6.7 - - - +
22A ALA* 5.7 0.7 - - + -
27A SER* 3.5 25.2 + - - +
29A TRP* 5.5 0.2 + - - -
30A GLN* 2.6 37.8 + - - +
137A ARG* 4.6 6.2 + - + -
138A VAL* 1.3 87.1 - - - +
140A GLY* 1.3 59.4 + - - +
155A LEU* 4.3 10.3 - - + -
156A GLN 3.3 13.2 - - - +
157A VAL* 3.9 19.1 - - + -
194A ASP* 4.7 3.8 - - - +
197A GLY* 4.4 12.1 - - - -
198A PRO* 3.8 12.4 + - - +
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Residues in contact with GLY 140 (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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16A ILE* 3.7 4.2 - - - +
30A GLN* 4.3 6.1 - - - -
139A THR* 1.3 75.5 - - - +
141A TRP* 1.3 59.0 + - - -
142A GLY 3.3 6.5 + - - -
155A LEU* 3.5 14.6 - - - +
156A GLN* 3.1 36.2 + - - +
193A GLY 5.7 0.2 - - - -
194A ASP* 3.4 16.6 - - - -
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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