Contacts of the helix formed by residues 128 - 136 (chain A) in PDB entry 6TT8
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 GLY 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A THR* 3.0 12.8 + - - -
95A ASP* 3.2 17.0 - - - -
98A THR* 3.2 27.5 + - - +
127A GLY* 1.3 79.5 - - - +
129A MET* 1.3 61.8 + - - -
131A ALA* 3.7 0.8 - - - +
132A LEU* 3.2 26.9 + - - +
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Residues in contact with MET 129 (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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91A THR* 4.2 6.7 - - - -
95A ASP* 3.4 1.0 + - - -
118A VAL* 4.0 18.6 - - + -
126A MET* 3.5 48.2 - - + +
127A GLY 3.6 1.2 - - - -
128A GLY* 1.3 75.5 - - - +
130A ASP* 1.3 67.5 + - - +
132A LEU* 3.2 6.9 + - - +
133A HIS* 3.1 29.6 + - + +
139A THR* 3.9 17.7 - - + +
155A VAL* 3.4 41.3 - - + +
156A ALA 4.2 0.9 - - - +
157A ALA* 3.8 32.3 - - + +
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Residues in contact with ASP 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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95A ASP* 3.0 16.4 + - - +
129A MET* 1.3 78.6 - - - +
131A ALA* 1.3 57.1 + - - +
133A HIS* 3.2 18.7 + - - +
134A ALA* 2.9 30.5 + - - +
155A VAL* 4.6 21.2 - - + +
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Residues in contact with ALA 131 (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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95A ASP* 2.9 43.6 + - + +
98A THR* 4.2 9.2 - - + -
99A ALA* 4.4 10.5 - - + +
102A LEU* 4.3 4.9 - - + +
128A GLY 3.7 7.6 - - - +
130A ASP* 1.3 77.1 - - - +
132A LEU* 1.3 57.5 + - - +
134A ALA* 3.3 7.5 + - - +
135A ALA* 3.0 27.7 + - - +
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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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88A VAL* 6.0 4.5 - - + -
91A THR* 3.5 27.1 - - + -
98A THR* 3.9 17.7 - - + -
102A LEU* 4.1 12.8 - - + -
116A ALA* 3.7 27.4 - - + -
118A VAL* 5.8 1.3 - - + -
128A GLY 3.2 10.3 - - - +
129A MET* 3.2 8.2 + - - +
131A ALA* 1.3 74.0 - - - +
133A HIS* 1.3 60.7 + - - +
135A ALA* 3.2 5.4 + - - -
136A GLY 3.0 9.2 + - - -
137A ILE* 2.9 52.7 + - + +
139A THR* 3.7 22.9 - - + -
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Residues in contact with HIS 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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129A MET* 3.1 23.3 + - + -
130A ASP* 3.2 18.3 + - - +
132A LEU* 1.3 76.1 - - - +
134A ALA* 1.3 61.6 + - - +
136A GLY* 3.4 11.3 + - - -
137A ILE 4.4 3.4 - - - +
139A THR* 2.8 38.6 + - + +
155A VAL* 3.7 18.7 - - + +
156A ALA 3.4 23.7 + - - -
157A ALA* 4.3 0.2 - - - -
158A GLN* 3.9 29.2 + - + +
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Residues in contact with ALA 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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130A ASP 2.9 16.9 + - - +
131A ALA* 3.6 7.9 - - - +
133A HIS* 1.3 77.3 - - - +
135A ALA* 1.3 59.6 + - - +
136A GLY* 3.2 1.0 + - - -
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Residues in contact with ALA 135 (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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102A LEU* 3.9 22.0 - - + -
131A ALA 3.0 16.7 + - - +
132A LEU 3.2 4.7 + - - +
134A ALA* 1.3 76.7 - - - +
136A GLY* 1.3 62.2 + - - +
137A ILE* 4.0 13.0 - - + +
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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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113A VAL 5.0 3.3 - - - +
132A LEU 3.0 2.6 + - - -
133A HIS 3.4 8.4 + - - -
134A ALA 3.2 4.4 - - - -
135A ALA* 1.3 81.5 - - - +
137A ILE* 1.3 61.9 + - - +
138A ALA 4.2 0.7 + - - -
158A GLN* 6.4 0.2 - - - -
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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