Contacts of the helix formed by residues 127 - 139 (chain V) in PDB entry 6QXT
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 PHE 127 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126V PHE* 1.3 72.9 - - - +
128V GLU* 1.3 70.3 + - - +
129V LYS 3.3 0.9 - - - -
130V SER 3.1 0.5 + - - -
131V GLN 2.9 14.6 + - - -
132V SER 3.3 2.4 + - - -
136i LEU* 5.3 6.3 - - + +
139i GLY 5.4 2.9 - - - +
146i SER* 2.6 42.6 - - - +
148i ARG* 3.3 26.9 - - + +
151i HIS* 3.7 7.0 - - + +
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Residues in contact with GLU 128 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127V PHE* 1.3 78.6 - - - +
129V LYS* 1.3 61.6 + - - +
132V SER* 2.2 43.2 + - - +
155V ILE* 5.9 1.0 - - - +
145i PRO 5.5 0.2 - - - -
146i SER* 4.5 3.1 - - - +
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Residues in contact with LYS 129 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121V LEU* 4.8 8.3 - - + -
126V PHE* 3.8 18.6 - - + +
127V PHE 3.3 0.4 - - - +
128V GLU* 1.3 82.5 - - - +
130V SER* 1.3 65.3 + - - +
132V SER* 4.0 0.2 - - - -
133V ILE* 3.0 21.2 + - - +
155V ILE* 4.6 13.7 - - - +
156V TYR* 5.6 2.7 - - - -
159V THR* 3.4 33.2 - - - -
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Residues in contact with SER 130 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117V GLN 5.2 0.2 - - - -
118V SER* 3.5 16.9 - - - +
121V LEU* 3.2 35.9 - - - -
122V GLY* 3.9 5.4 - - - -
126V PHE 2.9 24.4 + - - -
127V PHE 3.1 4.8 + - - -
129V LYS* 1.3 81.9 - - - +
131V GLN* 1.3 58.6 + - - -
133V ILE* 3.0 6.3 + - - +
134V MET 3.0 17.3 + - - -
146i SER 4.1 0.9 - - - -
147i ASN* 4.9 2.9 - - - -
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Residues in contact with GLN 131 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118V SER* 5.1 0.2 - - - -
127V PHE 2.9 7.5 + - - -
130V SER* 1.3 73.1 - - - +
132V SER* 1.3 61.4 + - - +
134V MET* 3.5 14.3 - - + +
135V GLU* 2.9 20.1 + - - +
144i ASP 3.0 28.5 - - - +
145i PRO* 3.1 15.6 - - - +
146i SER 3.0 23.1 - - - +
147i ASN* 4.0 6.3 - - + +
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Residues in contact with SER 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127V PHE 3.3 3.2 + - - -
128V GLU* 2.2 40.2 + - - -
129V LYS 4.0 0.2 - - - -
131V GLN* 1.3 76.9 - - - +
133V ILE* 1.3 57.6 + - - +
135V GLU* 3.1 8.4 + - - +
136V LEU* 2.9 26.9 + - - +
145i PRO 3.6 7.0 + - - -
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Residues in contact with ILE 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114V ILE* 4.5 10.0 - - - +
117V GLN* 5.0 7.0 - - + -
118V SER* 4.5 13.5 - - - +
129V LYS 3.0 15.4 + - - +
130V SER* 3.0 12.1 + - - +
132V SER* 1.3 75.2 - - - +
134V MET* 1.3 57.5 + - - +
136V LEU* 3.3 9.8 + - - +
137V TYR* 2.9 26.3 + - - +
152V SER* 4.7 21.1 - - - +
155V ILE* 6.2 2.5 - - + -
156V TYR* 6.3 1.6 - - + -
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Residues in contact with MET 134 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118V SER* 3.9 17.4 - - - -
130V SER 3.0 6.1 + - - -
131V GLN* 3.5 23.6 - - + +
132V SER 3.3 0.4 - - - -
133V ILE* 1.3 77.5 - - - +
135V GLU* 1.3 56.0 + - - +
137V TYR* 3.0 10.4 + - - +
138V HIS* 2.9 26.5 + - - +
144i ASP 5.0 3.1 - - - +
145i PRO* 5.5 0.9 - - + -
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Residues in contact with GLU 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131V GLN 2.9 15.3 + - - +
132V SER* 3.1 11.9 + - - +
134V MET* 1.3 73.7 - - - +
136V LEU* 1.3 60.3 + - - +
138V HIS* 3.1 8.4 + - - +
139V GLY* 2.9 24.3 + - - -
145i PRO* 4.4 16.3 - - + +
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Residues in contact with LEU 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114V ILE* 5.6 1.6 - - + -
132V SER 2.9 13.0 + - - +
133V ILE* 3.3 12.5 + - - +
135V GLU* 1.3 75.1 - - - +
137V TYR* 1.3 60.4 + - - +
139V GLY* 3.3 3.5 + - - +
140V LEU* 3.1 22.5 + - - +
148V ARG* 3.9 32.8 - - + +
151V HIS* 6.0 2.0 - - + -
152V SER* 4.8 7.4 - - - +
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Residues in contact with TYR 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111V ALA* 5.0 12.8 - - + +
114V ILE* 4.1 20.4 - - + +
115V LEU* 4.7 11.9 - - + +
133V ILE 2.9 13.8 + - - +
134V MET* 3.0 16.8 + - - +
136V LEU* 1.3 75.4 - - - +
138V HIS* 1.3 61.6 + - - +
139V GLY 3.4 0.7 + - - -
140V LEU* 3.4 18.0 + - - +
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Residues in contact with HIS 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134V MET 2.9 11.7 + - - +
135V GLU* 3.1 10.5 + - - +
137V TYR* 1.3 75.7 - - - +
139V GLY* 1.3 57.2 + - - +
140V LEU 3.4 3.4 + - - +
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Residues in contact with GLY 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135V GLU 2.9 13.3 + - - -
136V LEU* 3.3 6.9 + - - -
137V TYR 3.2 0.4 - - - -
138V HIS* 1.3 77.8 - - - +
140V LEU* 1.3 62.1 + - - +
141V GLU* 3.5 6.9 + - - +
146V SER* 5.5 5.9 - - - -
148V ARG* 5.2 4.1 - - - +
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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