Contacts of the helix formed by residues 127 - 141 (chain S) in PDB entry 2VGL
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 127 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ASP* 3.4 26.2 + - - +
247A TYR* 3.8 15.0 - - - +
90S VAL* 5.4 0.2 - - - -
125S GLU* 3.1 15.5 + - - +
126S THR* 1.3 77.6 + - - +
128S GLN* 1.3 62.2 + - - +
129S THR* 3.2 7.4 + - - +
130S LYS* 2.8 29.2 + - - +
131S VAL* 3.1 23.1 + - - +
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Residues in contact with GLN 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASP 4.8 1.8 + - - -
249A TYR* 3.9 10.9 - - - -
250A TYR* 5.5 0.2 - - - -
86S ASN* 2.6 31.3 + - - +
89S GLU* 2.7 48.8 + - - +
90S VAL* 3.8 24.0 - - + +
93S GLU* 6.2 0.3 - - - +
126S THR 4.3 0.2 - - - +
127S SER* 1.3 71.7 + - - +
129S THR* 1.3 57.8 + - - +
131S VAL* 4.2 0.3 - - - +
132S LEU* 3.0 35.6 + - + +
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Residues in contact with THR 129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASP* 3.7 26.0 - - - +
127S SER* 3.1 4.4 - - - +
128S GLN* 1.3 78.6 - - - +
130S LYS* 1.3 68.9 + - + +
132S LEU* 3.7 5.5 - - - +
133S LYS* 3.0 29.8 + - + +
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Residues in contact with LYS 130 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A HIS* 2.8 53.7 + - + +
246A ASP* 3.6 21.8 - - - +
247A TYR* 3.5 24.9 + - - +
125S GLU* 4.2 10.3 - - + +
127S SER* 2.8 19.1 + - - +
129S THR* 1.3 82.6 - - + +
131S VAL* 1.3 64.1 + - - +
133S LYS* 3.3 11.0 + - + +
134S GLN* 3.1 23.4 + - - +
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Residues in contact with VAL 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90S VAL* 3.8 27.6 - - + -
113S VAL* 5.0 1.1 - - + -
116S GLU* 4.1 20.2 - - + -
117S MET* 4.2 15.0 - - + -
125S GLU* 3.3 41.3 - - + +
127S SER 3.1 14.6 + - - +
128S GLN 4.2 2.7 - - - +
130S LYS* 1.3 72.6 - - - +
132S LEU* 1.3 68.0 + - - +
134S GLN* 3.1 6.2 + - - +
135S LEU* 2.9 32.6 + - + +
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Residues in contact with LEU 132 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90S VAL* 4.6 5.8 - - + +
93S GLU* 2.9 34.5 - - + -
94S TYR* 3.9 40.2 - - + +
128S GLN* 3.0 22.7 + - + +
129S THR* 3.7 5.8 - - - +
131S VAL* 1.3 78.2 - - - +
133S LYS* 1.3 62.6 + - - +
135S LEU* 3.1 6.1 + - + +
136S LEU* 2.9 47.0 + - + +
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Residues in contact with LYS 133 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129S THR* 3.0 19.8 + - + +
130S LYS* 3.6 11.7 - - + +
131S VAL 3.2 0.2 - - - -
132S LEU* 1.3 77.0 - - - +
134S GLN* 1.3 62.5 + - - +
136S LEU* 4.2 5.6 - - - +
137S MET* 3.2 23.1 + - - +
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Residues in contact with GLN 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 5.0 6.3 + - - +
163A SER* 5.2 13.9 + - - -
116S GLU* 3.7 33.6 + - + +
130S LYS 3.1 12.5 + - - +
131S VAL* 3.1 5.1 + - - +
132S LEU 3.1 0.6 - - - -
133S LYS* 1.3 80.4 - - - +
135S LEU* 1.3 59.2 + - - +
136S LEU 3.1 0.2 - - - -
137S MET* 3.2 27.6 + - - +
138S LEU* 2.8 50.9 + - + +
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Residues in contact with LEU 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90S VAL* 3.9 11.4 - - + -
94S TYR* 3.8 34.9 + - + +
112S THR* 3.8 28.7 - - + -
113S VAL* 3.7 36.1 - - + -
116S GLU* 4.6 8.7 - - - +
131S VAL* 2.9 38.8 + - + +
132S LEU* 3.6 6.7 - - - +
134S GLN* 1.3 76.1 - - - +
136S LEU* 1.3 59.1 + - - +
138S LEU* 3.6 6.2 + - + +
139S GLN* 3.1 28.8 + - - +
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Residues in contact with LEU 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94S TYR* 4.5 13.2 - - + +
96S HIS* 6.2 2.9 - - + +
132S LEU* 2.9 40.2 + - + +
133S LYS* 4.2 4.7 - - - +
135S LEU* 1.3 77.2 - - - +
137S MET* 1.3 69.2 + - - +
139S GLN* 3.5 31.5 + - - +
140S SER* 3.5 14.4 + - - -
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Residues in contact with MET 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PRO* 6.5 0.4 - - + -
126A THR* 3.8 18.8 - - - +
133S LYS* 3.2 16.3 + - - +
134S GLN* 3.2 36.2 + - - +
136S LEU* 1.3 77.9 - - - +
138S LEU* 1.3 68.6 + - + +
140S SER* 2.8 25.7 + - - +
141S LEU* 3.4 30.3 + - + +
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Residues in contact with LEU 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.4 44.2 - - + +
89A THR* 5.5 0.5 - - - +
126A THR* 3.4 32.8 - - + -
112S THR* 3.8 28.7 - - + -
116S GLU* 3.9 15.7 - - - +
134S GLN* 2.8 44.6 + - + +
135S LEU* 3.8 7.9 - - - +
137S MET* 1.3 78.0 - - + +
139S GLN* 1.3 61.3 + - - +
140S SER 3.3 0.9 + - - -
141S LEU* 3.5 11.3 + - + +
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Residues in contact with GLN 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94S TYR* 3.0 49.2 + - - +
95S PHE* 6.1 0.8 - - - -
109S LYS* 4.6 16.2 - - - +
135S LEU 3.1 13.8 + - - +
136S LEU* 3.7 23.0 - - - +
137S MET 3.1 0.4 + - - -
138S LEU* 1.3 76.7 - - - +
140S SER* 1.3 61.0 + - - +
141S LEU 3.7 5.6 - - - +
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Residues in contact with SER 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136S LEU 3.5 10.3 + - - -
137S MET* 2.8 23.8 + - - +
139S GLN* 1.3 76.9 - - - +
141S LEU* 1.3 69.2 + - - +
142S GLU* 4.2 7.1 - - - +
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Residues in contact with LEU 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 3.8 37.9 - - + -
89A THR* 4.2 7.9 - - - +
126A THR* 4.1 14.6 - - + +
127A PHE* 5.7 2.0 - - + -
137S MET* 3.8 32.1 - - + +
138S LEU* 3.7 11.3 - - + +
139S GLN 3.4 8.9 - - - +
140S SER* 1.3 86.0 + - - +
142S GLU* 1.3 64.1 + - - +
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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