Contacts of the helix formed by residues 115 - 127 (chain A) in PDB entry 2VF8
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 THR 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLY 2.8 9.5 + - - -
112A SER* 3.2 10.5 + - - +
113A VAL 4.0 3.6 - - - +
114A THR* 1.3 80.2 + - - +
116A LEU* 1.3 63.8 + - - +
117A SER 3.2 0.4 - - - -
118A ASN* 3.0 25.2 + - - +
119A LEU* 3.4 16.7 + - - +
359A ARG* 5.1 1.4 + - - -
392A THR* 4.0 15.9 - - + -
395A TYR* 4.4 10.3 - - + -
75B ARG* 3.4 46.0 - - - +
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Residues in contact with LEU 116 (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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111A GLY* 2.8 3.6 + - - -
114A THR* 2.7 32.2 + - + +
115A THR* 1.3 71.5 + - - +
117A SER* 1.3 63.9 + - - +
119A LEU* 2.9 17.5 + - + +
120A LEU* 3.1 16.6 + - + +
317A LEU* 4.8 11.2 - - + -
356A LEU* 3.8 25.8 - - + +
359A ARG* 4.1 30.3 - - + -
360A LEU* 4.3 19.1 - - + -
363A LEU* 3.4 30.7 - - + -
373A LEU* 4.4 13.2 - - + -
395A TYR* 4.3 0.4 - - - +
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Residues in contact with SER 117 (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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109A SER* 3.5 8.0 + - - -
111A GLY* 2.9 37.0 + - - -
112A SER* 3.2 2.5 + - - -
116A LEU* 1.3 75.1 - - - +
118A ASN* 1.3 60.1 + - - +
120A LEU* 2.9 25.0 - - - +
121A ARG* 3.2 17.5 + - - +
309A ILE* 4.7 0.2 - - - +
313A SER* 5.7 1.0 + - - -
373A LEU* 4.4 11.5 + - - +
1847A SO4 3.5 20.4 - - - -
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Residues in contact with ASN 118 (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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112A SER* 5.7 0.6 - - - +
115A THR* 3.0 15.8 + - - +
117A SER* 1.3 77.3 - - - +
119A LEU* 1.3 65.5 + - - +
120A LEU 3.5 0.2 - - - -
121A ARG* 3.4 35.6 + - - +
122A MET* 3.1 41.5 + - - +
139A ALA* 6.0 0.9 - - - +
140A GLU* 4.7 7.8 - - - +
1847A SO4 5.1 2.5 - - - +
75B ARG* 5.8 6.5 - - - +
78B ASN* 5.4 6.9 + - - +
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Residues in contact with LEU 119 (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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115A THR* 3.8 16.4 - - - +
116A LEU* 2.9 12.3 + - + +
118A ASN* 1.3 85.0 - - - +
120A LEU* 1.3 63.1 + - - +
121A ARG 3.3 0.2 - - - -
122A MET* 3.7 21.6 + - + +
123A LEU* 3.3 20.1 + - - +
352A MET* 3.7 12.1 - - + +
355A ASP* 3.6 18.8 - - - +
356A LEU* 4.3 22.6 - - + +
359A ARG* 3.7 35.7 - - - +
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Residues in contact with LEU 120 (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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116A LEU 3.1 14.1 + - - +
117A SER* 2.9 26.0 - - - +
119A LEU* 1.3 77.5 - - - +
121A ARG* 1.3 54.6 - - - +
122A MET 3.2 0.4 - - - -
123A LEU* 3.6 12.3 - - + -
124A TYR* 2.5 45.2 + - + -
309A ILE* 3.8 30.3 - - + -
312A LEU* 4.0 30.3 - - + -
313A SER* 4.5 6.3 - - - +
320A VAL* 5.7 2.7 - - + -
324A LEU* 6.1 2.0 - - + -
356A LEU* 4.0 21.0 - - + +
373A LEU* 4.7 11.9 - - + -
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Residues in contact with ARG 121 (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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117A SER* 3.2 16.9 + - - +
118A ASN* 3.4 43.4 + - - +
120A LEU* 1.3 76.4 - - - +
122A MET* 1.3 64.3 + - - +
124A TYR* 4.7 0.2 - - - -
125A SER* 3.1 22.3 + - - -
139A ALA* 3.5 17.4 + - + +
140A GLU* 3.8 24.4 + - - +
142A PHE* 3.3 48.8 - - + +
143A SER* 3.7 13.6 + - - +
144A PRO* 5.4 1.2 - - - +
309A ILE* 3.8 11.6 - - + +
1847A SO4 2.6 49.5 + - - -
76B LEU* 5.6 0.2 - - - +
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Residues in contact with MET 122 (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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118A ASN* 3.1 29.1 + - - +
119A LEU* 3.8 21.5 - - + +
120A LEU 3.2 0.2 - - - -
121A ARG* 1.3 76.6 - - - +
123A LEU* 1.3 57.0 + - - +
125A SER* 3.1 4.9 + - - -
126A ARG* 3.0 29.3 + - - +
139A ALA* 4.0 21.1 - - + +
351A ARG* 5.3 8.1 - - - +
352A MET* 3.6 23.5 - - + +
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Residues in contact with LEU 123 (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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119A LEU 3.3 10.2 + - - +
120A LEU* 3.0 12.5 + - + +
122A MET* 1.3 76.1 - - - +
124A TYR* 1.3 75.3 + - + +
125A SER 2.9 5.5 + - - -
127A ALA* 3.0 33.3 + - + +
304A PHE* 3.9 36.6 - - + -
324A LEU* 4.6 12.3 - - + -
349A LEU* 5.5 3.8 - - + +
352A MET* 3.4 31.6 - - + +
353A ALA* 4.5 8.5 - - + +
356A LEU* 3.6 29.6 - - + -
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Residues in contact with TYR 124 (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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120A LEU* 2.5 41.1 + - + +
121A ARG 3.9 2.0 - - - +
123A LEU* 1.3 81.4 - - + +
125A SER* 1.3 56.0 + - - +
127A ALA 2.7 16.1 - - - +
128A GLY* 4.7 1.3 - - - -
130A TYR* 3.7 3.6 + - - -
142A PHE* 3.7 23.2 - + + -
302A VAL* 3.5 38.2 - - + +
303A THR 4.1 1.1 - - - -
304A PHE* 3.5 27.5 + + + +
307A LEU* 3.2 27.8 + - - +
308A ASP* 3.4 11.1 + - - -
309A ILE* 3.5 42.2 - - + -
312A LEU* 3.6 23.3 - - + +
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Residues in contact with SER 125 (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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121A ARG 3.1 12.6 + - - -
122A MET* 3.1 10.0 + - - -
123A LEU 2.9 2.0 - - - -
124A TYR* 1.3 76.9 - - - +
126A ARG* 1.3 70.4 + - - +
127A ALA 3.1 3.3 - - - +
130A TYR* 2.8 23.3 + - - -
136A ILE* 4.4 7.6 - - - +
137A VAL 2.3 32.6 + - - -
138A TYR* 3.6 2.3 - - - -
139A ALA* 3.5 16.2 + - - -
142A PHE* 3.9 0.9 - - - -
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Residues in contact with ARG 126 (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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122A MET 3.0 16.0 + - - +
125A SER* 1.3 76.8 - - - +
127A ALA* 1.3 62.4 + - + +
128A GLY 4.9 0.2 - - - +
130A TYR* 4.4 5.0 - - - -
136A ILE* 5.1 5.0 - - - +
344A GLU* 3.5 31.9 + - - +
345A GLN* 4.1 26.5 + - + +
348A ALA* 4.2 25.5 - - + +
349A LEU 5.6 0.7 - - - +
351A ARG* 5.3 4.4 - - - +
352A MET* 4.3 13.9 - - - -
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Residues in contact with ALA 127 (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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123A LEU* 3.0 23.7 + - + +
124A TYR 2.7 20.4 - - - +
125A SER 3.1 2.6 - - - +
126A ARG* 1.3 83.2 - - + +
128A GLY* 1.3 67.6 + - - +
130A TYR* 3.9 0.2 - - - -
304A PHE* 4.8 0.2 - - + -
338A ARG* 5.2 0.2 - - - +
345A GLN* 4.2 14.4 - - + +
349A LEU* 3.8 40.8 - - + -
352A MET* 5.5 1.6 - - - -
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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