Contacts of the helix formed by residues 116 - 131 (chain A) in PDB entry 1VDV
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 CYS 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A CYS 6.0 0.2 - - - +
49A GLY 5.9 0.2 - - - -
50A ALA* 5.1 8.8 - - + +
110A GLY 5.4 0.9 - - - -
114A GLY 3.3 0.2 - - - -
115A PHE* 1.3 77.7 - - - +
117A THR* 1.3 71.2 + - - +
118A PRO 3.4 1.8 - - - -
119A GLY* 3.3 5.9 + - - +
120A ILE* 3.1 42.4 + - + +
146A ASN* 5.3 0.2 + - - -
147A LEU 3.4 21.1 - - - +
148A CYS* 3.7 8.1 - - - -
156A ILE* 5.0 2.9 - - - -
744A LEU* 4.2 7.0 - - + -
3001A FES 2.4 41.3 - - - -
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Residues in contact with THR 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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105A ILE* 4.0 20.4 - - + -
110A GLY 4.8 0.7 + - - -
111A SER* 2.8 29.4 + - - +
114A GLY* 3.3 13.7 + - - -
116A CYS* 1.3 86.2 - - - +
118A PRO* 1.3 65.4 - - - +
120A ILE* 3.2 4.6 + - - +
121A VAL* 2.8 40.5 + - + +
585A GLN 3.6 4.3 - - - -
586A ALA* 3.5 31.4 - - + +
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Residues in contact with PRO 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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38A GLY 3.3 26.9 - - - +
39A THR* 5.1 3.1 - - - -
40A LYS* 4.7 6.7 - - + -
50A ALA 5.2 2.0 - - - +
52A THR 5.1 0.7 - - - -
88A VAL* 4.0 18.4 - - + -
114A GLY 3.4 11.4 - - - +
115A PHE 3.9 7.2 - - - +
116A CYS 3.7 3.4 - - - -
117A THR* 1.3 93.6 - - - +
119A GLY* 1.3 57.6 + - - +
121A VAL* 3.1 9.2 + - + +
122A MET* 2.9 35.5 + - + +
585A GLN 3.5 14.4 - - - +
588A GLY* 4.1 13.0 - - - +
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Residues in contact with GLY 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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49A GLY 3.3 20.0 - - - -
50A ALA 4.1 10.9 + - - -
52A THR* 3.4 16.9 - - - -
116A CYS 3.3 6.3 + - - -
117A THR 3.3 0.8 - - - -
118A PRO* 1.3 79.8 - - - +
120A ILE* 1.3 57.3 + - - +
122A MET 3.5 0.3 + - - -
123A SER* 3.1 21.5 + - - -
146A ASN* 3.2 15.1 + - - -
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Residues in contact with ILE 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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105A ILE* 3.9 12.3 - - + -
116A CYS* 3.1 41.8 + - + +
117A THR* 3.9 4.7 - - - +
119A GLY* 1.3 72.8 - - - +
121A VAL* 1.3 66.4 + - - +
123A SER* 3.2 0.8 + - - -
124A MET* 3.0 21.1 + - - +
143A PHE* 3.5 19.6 - - + -
146A ASN* 3.6 28.7 - - + +
147A LEU 4.5 1.6 - - - +
148A CYS* 4.4 4.9 - - + -
156A ILE* 3.9 16.6 - - + -
160A PHE* 3.9 16.4 - - + -
1232A PHE* 3.8 22.4 - - + -
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Residues in contact with VAL 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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88A VAL* 4.2 8.7 - - + -
91A ILE* 3.5 30.1 - - + -
101A VAL* 3.6 21.8 - - + +
102A GLN* 3.9 9.6 - - + -
105A ILE* 4.1 17.0 - - + -
117A THR* 2.8 36.5 + - + +
118A PRO* 3.3 7.2 - - + +
120A ILE* 1.3 77.8 - - - +
122A MET* 1.3 59.3 + - - +
124A MET* 3.3 0.4 + - - -
125A TYR* 2.8 27.7 + - - +
160A PHE* 5.0 0.7 - - - -
586A ALA* 3.8 16.4 - - + +
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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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52A THR* 3.5 37.0 - - + +
53A VAL* 4.3 3.4 - - - -
54A MET* 4.0 12.3 - - + +
86A THR* 3.3 27.6 - - + +
87A THR 3.7 5.6 - - - +
88A VAL* 3.6 34.1 - - + +
91A ILE* 4.2 15.3 - - + -
118A PRO 2.9 18.3 + - - +
119A GLY 3.9 0.2 - - - +
121A VAL* 1.3 77.4 - - - +
123A SER* 1.3 59.2 + - - +
125A TYR* 3.8 24.9 - - + +
126A THR* 2.8 34.5 + - - -
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Residues in contact with SER 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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52A THR* 3.7 6.2 - - - +
69A SER* 5.0 4.7 + - - -
119A GLY 3.1 12.2 + - - -
120A ILE 3.2 7.6 + - - -
122A MET* 1.3 76.9 - - - +
124A MET* 1.3 63.1 + - - +
126A THR* 3.5 5.3 + - - -
127A LEU* 3.2 21.1 + - - +
142A ALA* 3.7 20.0 + - - +
143A PHE* 3.8 8.1 - - - -
146A ASN* 2.7 28.3 + - - -
341A GLN* 3.4 13.5 + - - -
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Residues in contact with MET 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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101A VAL* 3.9 12.8 - - + -
120A ILE 3.0 16.2 + - - +
121A VAL 3.7 3.4 - - - +
123A SER* 1.3 74.5 - - - +
125A TYR* 1.3 65.5 + - - +
127A LEU* 3.1 25.2 + - + +
128A LEU* 3.1 47.4 + - + +
139A ILE* 4.2 19.3 - - + -
142A ALA* 5.1 0.7 - - - -
143A PHE* 3.8 12.9 - - + -
160A PHE* 3.8 48.5 - - + -
163A PHE* 3.7 24.9 - - + -
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Residues in contact with TYR 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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54A MET* 3.5 23.5 - - + +
86A THR* 4.3 5.2 - - + +
91A ILE* 3.5 37.1 - - + +
99A HIS* 3.4 28.5 - + - -
101A VAL* 4.2 8.3 - - + +
121A VAL 2.8 22.1 + - - +
122A MET* 3.8 21.1 - - + +
124A MET* 1.3 73.0 - - - +
126A THR* 1.3 64.3 - - - +
128A LEU* 3.1 7.3 + - + +
129A ARG* 3.0 54.2 + - + +
209A GLU* 2.7 32.7 + - - -
210A PRO* 3.8 9.5 - - - +
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Residues in contact with THR 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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53A VAL 4.7 0.2 + - - -
54A MET* 3.5 32.0 - - + +
68A PHE* 3.7 10.1 - - - +
69A SER* 3.6 36.5 - - - +
122A MET 2.8 22.5 + - - -
123A SER 3.7 4.7 - - - -
125A TYR* 1.3 76.8 - - - +
127A LEU* 1.3 64.1 + - - +
129A ARG* 3.2 10.0 + - - +
130A ASN* 3.0 33.5 + - - +
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Residues in contact with LEU 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 SER 3.2 9.8 + - - +
124A MET* 3.1 20.3 + - + +
126A THR* 1.3 80.2 - - - +
128A LEU* 1.3 50.5 + - - +
130A ASN* 3.0 11.5 + - + +
131A GLN* 2.6 39.3 + - + +
134A PRO* 3.9 26.2 - - + -
138A GLU* 3.5 35.9 - - + +
139A ILE* 3.7 19.7 - - + -
142A ALA* 4.0 12.1 - - + -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A HIS* 4.8 1.1 - - + -
101A VAL* 3.5 31.2 - - + -
124A MET* 3.1 26.5 + - + +
125A TYR* 3.6 8.5 - - + +
127A LEU* 1.3 78.8 - - - +
129A ARG* 1.3 64.4 + - - +
131A GLN 3.5 14.6 - - - +
132A PRO* 3.2 34.2 - - - +
134A PRO* 3.7 19.3 - - + -
163A PHE* 4.0 26.5 - - + -
204A LEU* 4.0 24.0 - - + +
206A PRO* 6.1 0.7 - - - +
209A GLU* 6.2 0.2 - - - +
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Residues in contact with ARG 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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54A MET* 3.8 23.8 - - - +
67A HIS* 3.8 42.3 + - + -
125A TYR* 3.0 60.9 + - + +
126A THR 3.2 7.8 + - - +
128A LEU* 1.3 79.6 - - - +
130A ASN* 1.3 59.7 + - - +
132A PRO* 5.2 2.1 - - - +
206A PRO* 5.7 2.0 + - - +
209A GLU* 3.9 36.6 - - - +
210A PRO* 4.3 14.1 + - - +
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Residues in contact with ASN 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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67A HIS* 3.0 38.4 + - - +
126A THR* 3.0 29.5 + - - +
127A LEU* 3.0 12.1 + - + +
129A ARG* 1.3 81.5 - - - +
131A GLN* 1.3 62.4 + - + +
132A PRO* 4.1 4.5 - - - +
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Residues in contact with GLN 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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127A LEU* 2.6 27.2 + - + +
128A LEU* 3.4 7.8 - - - +
130A ASN* 1.3 78.0 - - + +
132A PRO* 1.3 74.0 - - - +
133A GLU* 2.8 41.5 + - - +
134A PRO* 3.1 32.8 - - + +
138A GLU* 4.0 14.1 - - - +
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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