Contacts of the helix formed by residues 122 - 136 (chain A) in PDB entry 2YVL
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 VAL 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLU* 3.0 12.6 + - - +
121A ALA* 1.3 79.7 - - + +
123A GLU* 1.3 59.4 + - - +
124A GLU* 4.1 12.1 - - + +
125A PHE* 3.0 37.5 + - + -
126A TYR* 2.9 23.7 + - - +
146A ASN* 3.8 1.1 - - - -
601A SAM 3.5 19.3 - - - +
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Residues in contact with GLU 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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121A ALA 3.7 1.8 + - - -
122A VAL* 1.3 70.6 - - - +
124A GLU* 1.3 64.3 + - + +
126A TYR* 3.6 3.6 - - + +
127A LYS* 2.9 67.1 + - - +
146A ASN* 3.0 34.1 - - - +
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Residues in contact with GLU 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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71A LYS* 2.7 39.8 + - - +
122A VAL* 3.3 8.9 - - + +
123A GLU* 1.3 84.0 - - + +
125A PHE* 1.3 65.9 + - + +
127A LYS* 3.7 7.0 + - - +
128A THR* 2.8 35.5 + - - -
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Residues in contact with PHE 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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71A LYS* 3.6 41.5 - - + -
72A THR* 3.5 15.5 - - + -
101A GLY 3.1 24.5 - - - +
120A GLU* 3.8 8.5 - - + +
122A VAL* 3.0 36.2 + - + +
124A GLU* 1.3 91.2 - - + +
126A TYR* 1.3 59.6 + - - +
128A THR* 3.2 4.9 + - - -
129A ALA* 2.9 27.0 + - - +
601A SAM 3.4 23.3 - - - -
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Residues in contact with TYR 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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100A THR* 5.6 1.8 - - - -
120A GLU* 3.5 17.5 - - + +
122A VAL 2.9 15.5 + - - +
123A GLU* 3.6 12.8 - - + +
125A PHE* 1.3 77.2 - - - +
127A LYS* 1.3 76.5 + - + +
129A ALA* 3.8 5.2 + - - +
130A GLN* 3.1 51.3 + - - +
144A PHE* 3.7 30.2 + + + +
145A PHE 3.8 5.8 - - - -
146A ASN* 3.6 50.9 + - + +
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Residues in contact with LYS 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 GLU* 2.9 53.7 + - - +
124A GLU* 3.9 6.7 - - - +
126A TYR* 1.3 93.8 - - + +
128A THR* 1.3 58.5 + - - +
130A GLN* 3.4 10.3 + - - +
131A LYS* 3.0 28.3 + - - +
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Residues in contact with THR 128 (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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69A GLU* 3.7 42.8 + - + +
71A LYS* 3.3 37.0 + - + +
102A SER* 4.9 4.0 - - - +
124A GLU 2.8 23.3 + - - -
125A PHE* 3.2 6.9 + - - -
127A LYS* 1.3 73.3 - - - +
129A ALA* 1.3 60.7 + - - +
131A LYS* 3.3 7.9 + - + +
132A ASN* 2.8 33.1 + - - +
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Residues in contact with ALA 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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100A THR* 3.7 25.6 - - + -
101A GLY 3.6 13.0 + - - +
102A SER 3.6 18.2 - - - -
103A GLY* 3.8 2.0 - - - +
106A LEU* 5.0 0.2 - - + -
125A PHE 2.9 17.9 + - - +
126A TYR 4.0 4.7 - - - +
128A THR* 1.3 78.2 - - - +
130A GLN* 1.3 60.6 + - - +
132A ASN* 3.5 0.5 + - - +
133A LEU* 3.2 32.3 + - - +
144A PHE* 4.4 5.6 - - + -
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Residues in contact with GLN 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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126A TYR* 3.1 56.3 + - - +
127A LYS* 3.4 12.0 + - - +
128A THR 3.3 0.4 - - - -
129A ALA* 1.3 73.2 - - - +
131A LYS* 1.3 65.6 + - - +
133A LEU* 4.2 0.5 - - - +
134A LYS* 3.1 28.2 + - - +
144A PHE* 3.6 46.6 - - + +
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Residues in contact with LYS 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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69A GLU* 4.6 16.8 - - - +
127A LYS 3.0 17.9 + - - +
128A THR* 3.3 8.3 + - + +
130A GLN* 1.3 75.0 - - - +
132A ASN* 1.3 66.1 + - - +
134A LYS* 4.2 2.6 - - - +
135A LYS* 3.0 41.4 + - + +
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Residues in contact with ASN 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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67A GLY 4.5 1.6 - - - +
68A PHE* 3.5 29.5 - - + -
69A GLU* 2.8 52.0 + - - +
102A SER 2.8 25.3 + - - +
128A THR* 2.8 25.4 + - - +
129A ALA 3.7 4.7 - - - +
130A GLN 3.4 0.2 - - - -
131A LYS* 1.3 75.0 - - - +
133A LEU* 1.3 62.4 + - - +
135A LYS* 3.4 9.5 - - - +
136A PHE* 3.3 26.7 - - - -
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Residues in contact with LEU 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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68A PHE* 3.7 17.5 - - + -
103A GLY* 3.5 30.5 - - - +
106A LEU* 3.8 29.2 - - + -
107A ALA* 4.2 12.3 - - - +
110A SER* 4.6 1.6 - - - -
129A ALA 3.2 24.8 + - - +
130A GLN 4.2 2.5 - - - +
132A ASN* 1.3 78.7 - - - +
134A LYS* 1.3 58.8 + - - +
136A PHE* 3.2 3.5 + - - -
137A ASN 3.1 4.2 + - - -
138A LEU* 2.8 46.5 + - + +
139A GLY* 3.7 27.4 - - - +
142A VAL* 4.7 0.4 - - + -
144A PHE* 4.5 8.3 - - + -
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Residues in contact with LYS 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 GLN 3.1 18.9 + - - +
131A LYS* 4.2 2.7 - - - +
133A LEU* 1.3 75.7 - - - +
135A LYS* 1.3 65.0 + - - +
137A ASN* 3.0 16.8 + - - +
138A LEU 3.9 8.0 + - - +
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Residues in contact with LYS 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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9A TYR* 2.7 49.6 + - + -
67A GLY 4.4 8.7 + - - +
131A LYS* 3.0 33.7 + - + +
132A ASN* 3.4 12.3 - - - +
134A LYS* 1.3 76.5 - - - +
136A PHE* 1.3 83.6 + - + +
137A ASN 3.5 0.2 - - - -
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Residues in contact with PHE 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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9A TYR* 3.8 31.0 - + + -
20A LEU* 4.1 8.7 - - + -
58A PRO* 5.1 2.5 - - + -
63A ILE* 3.5 50.1 - - + +
67A GLY* 3.8 34.1 - - - -
68A PHE* 4.0 4.7 - + - -
132A ASN* 3.3 20.0 - - - +
133A LEU 3.2 3.0 + - - +
134A LYS 3.1 0.6 - - - -
135A LYS* 1.3 110.4 - - + +
137A ASN* 1.3 69.7 + - - +
138A LEU* 3.3 20.2 + - + +
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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