Contacts of the helix formed by residues 122 - 136 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D GLU* 3.0 9.1 + - - +
121D ALA* 1.3 77.4 - - + +
123D GLU* 1.3 66.0 + - - +
124D GLU* 3.9 16.6 - - + +
125D PHE* 3.3 37.5 + - + -
126D TYR* 3.1 18.0 + - - +
146D ASN* 3.8 1.1 - - - -
603D SAM 3.6 17.3 - - - +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA 3.6 4.4 + - - -
122D VAL* 1.3 70.9 - - - +
124D GLU* 1.3 65.9 + - - +
126D TYR* 3.4 9.2 + - + +
127D LYS* 3.0 42.4 + - + +
146D ASN* 3.4 31.3 + - - +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LYS* 3.6 36.0 + - + +
122D VAL* 3.3 10.6 - - + +
123D GLU* 1.3 79.6 - - - +
125D PHE* 1.3 72.4 + - + +
127D LYS* 3.5 7.0 + - - +
128D THR* 2.8 30.1 + - - -
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Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LYS* 3.5 34.8 - - + -
72D THR* 3.7 16.4 - - + -
101D GLY 3.0 24.2 - - - +
120D GLU* 3.8 7.6 - - + -
122D VAL* 3.3 38.3 + - + +
123D GLU 3.3 0.2 - - - -
124D GLU* 1.3 94.4 - - + +
126D TYR* 1.3 58.0 + - - +
128D THR* 3.6 4.9 - - - -
129D ALA* 2.8 31.2 + - - +
603D SAM 3.2 27.1 - - - -
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Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 5.7 1.3 - - - -
120D GLU* 3.6 16.2 - - + +
122D VAL 3.1 13.2 + - - +
123D GLU* 3.4 14.4 - - + +
125D PHE* 1.3 77.0 - - - +
127D LYS* 1.3 84.7 + - - +
129D ALA* 4.2 4.8 - - - +
130D GLN* 3.2 48.9 + - - +
144D PHE* 3.6 38.3 + + + +
145D PHE 4.0 4.7 - - - -
146D ASN* 3.5 49.9 + - + +
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLU* 3.0 39.1 + - + +
124D GLU* 3.7 6.5 - - - +
126D TYR* 1.3 94.7 + - + +
128D THR* 1.3 60.7 + - - +
130D GLN* 3.5 15.3 + - + +
131D LYS* 2.9 29.4 + - - +
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Residues in contact with THR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU* 4.0 25.0 + - + +
71D LYS* 3.3 37.7 - - + +
101D GLY 5.2 0.7 - - - -
102D SER* 4.7 4.9 - - - +
124D GLU* 2.8 20.8 + - - +
125D PHE* 3.2 9.2 + - - -
127D LYS* 1.3 74.8 - - - +
129D ALA* 1.3 55.0 + - - +
131D LYS* 3.2 9.3 + - - +
132D ASN* 2.8 49.8 + - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 3.7 25.8 - - + -
101D GLY 3.6 13.0 + - - +
102D SER 3.5 19.3 - - - -
103D GLY* 3.8 3.1 - - - +
106D LEU* 4.9 0.2 - - + -
125D PHE 2.8 19.5 + - - +
126D TYR* 4.2 4.0 - - - +
128D THR* 1.3 72.3 - - - +
130D GLN* 1.3 63.3 + - - +
132D ASN 3.3 1.2 + - - -
133D LEU* 3.1 31.1 + - - +
144D PHE* 4.3 5.8 - - + -
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Residues in contact with GLN 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.2 47.1 + - - +
127D LYS* 3.6 18.8 + - - +
128D THR 3.3 0.4 - - - -
129D ALA* 1.3 78.9 - - - +
131D LYS* 1.3 56.6 + - - +
133D LEU* 3.4 1.2 + - - +
134D LYS* 2.9 42.8 + - + +
144D PHE* 3.5 48.4 - - + +
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Residues in contact with LYS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU* 2.6 33.1 + - - +
127D LYS 2.9 17.7 + - - +
128D THR* 3.4 9.2 + - - +
130D GLN* 1.3 74.6 - - - +
132D ASN* 1.3 89.2 + - - +
134D LYS* 3.9 4.9 - - - +
135D LYS* 2.9 54.8 + - + +
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Residues in contact with ASN 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D GLY 4.7 0.7 - - - +
68D PHE* 3.5 29.9 - - + -
69D GLU* 2.9 45.8 + - - +
102D SER 2.8 22.5 + - - +
128D THR* 2.8 26.2 + - - +
129D ALA 3.3 5.8 + - - +
131D LYS* 1.3 91.2 - - - +
133D LEU* 1.3 60.4 + - - +
135D LYS* 3.6 3.1 - - - +
136D PHE* 3.3 29.5 - - - -
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PHE* 3.7 18.4 - - + -
103D GLY* 3.5 25.8 - - - +
106D LEU* 3.8 34.5 - - + +
107D ALA* 4.0 14.6 - - + -
110D SER* 4.6 1.6 - - - -
129D ALA 3.1 26.7 + - - +
130D GLN 4.1 2.0 - - - +
132D ASN* 1.3 74.6 - - - +
134D LYS* 1.3 66.9 + - - +
136D PHE 3.2 2.6 + - - -
137D ASN 3.2 4.2 + - - -
138D LEU* 2.8 44.3 + - + +
139D GLY* 3.7 26.7 - - - +
144D PHE* 4.7 4.9 - - + -
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Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLN* 2.9 31.4 + - + +
131D LYS* 3.9 4.5 - - - +
133D LEU* 1.3 78.5 - - - +
135D LYS* 1.3 62.6 + - - +
136D PHE 3.3 0.7 + - - -
137D ASN* 3.3 11.9 + - - +
138D LEU 3.1 27.5 + - - +
139D GLY 3.5 20.9 + - - -
140D LYS* 4.1 12.3 - - - +
144D PHE* 4.8 13.0 - - - -
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Residues in contact with LYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 3.1 47.4 + - + -
67D GLY 4.7 8.6 + - - +
131D LYS* 2.9 42.2 + - + +
132D ASN* 3.6 7.9 - - - +
133D LEU 3.2 0.2 - - - -
134D LYS* 1.3 78.3 - - - +
136D PHE* 1.3 82.1 + - + +
137D ASN 3.5 0.6 + - - -
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Residues in contact with PHE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 4.1 31.2 - + + -
20D LEU* 4.3 6.3 - - + -
58D PRO* 5.3 2.9 - - + -
63D ILE* 3.6 48.4 - - + +
67D GLY* 3.7 39.9 - - - -
68D PHE* 3.9 5.2 - + - -
132D ASN* 3.3 23.8 - - - +
133D LEU 3.2 3.9 + - - +
134D LYS 3.2 0.6 - - - -
135D LYS* 1.3 105.4 - - + +
137D ASN* 1.3 70.9 + - - +
138D LEU* 3.4 17.1 + - + +
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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