Contacts of the helix formed by residues 103 - 113 (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 GLY 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D PHE* 3.2 14.3 - - - -
100D THR* 3.1 14.8 + - - -
101D GLY 3.4 0.8 - - - -
102D SER* 1.3 77.8 - - - +
104D ALA* 1.3 59.5 + - - +
105D LEU 3.5 1.6 - - - -
106D LEU* 3.7 16.4 - - - -
107D ALA 3.0 23.6 + - - -
129D ALA* 3.8 11.4 - - - +
133D LEU* 3.5 7.6 - - - +
603D SAM 3.5 0.4 + - - -
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Residues in contact with ALA 104 (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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64D ILE* 3.7 36.0 - - + +
68D PHE* 4.0 13.2 - - + -
74D ILE* 3.6 23.3 - - + -
75D ILE 3.4 21.9 - - - +
80D SER* 4.6 0.7 + - - -
102D SER 3.4 2.0 + - - -
103D GLY* 1.3 79.1 - - - +
105D LEU* 1.3 62.6 + - - +
107D ALA 3.7 2.1 + - - -
108D VAL* 3.7 5.7 - - - +
603D SAM 3.4 10.7 + - - +
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Residues in contact with LEU 105 (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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75D ILE* 3.8 17.6 + - + -
80D SER* 3.6 31.0 - - - +
83D ILE* 4.0 25.8 - - + -
97D GLU* 3.4 25.4 - - + +
104D ALA* 1.3 73.5 - - - +
106D LEU* 1.3 67.0 - - - +
108D VAL* 3.0 16.3 + - + +
109D LEU* 3.0 26.1 + - + +
163D PHE* 3.4 34.8 - - + -
165D ASP* 5.7 0.2 - - + -
603D SAM 3.1 18.1 + - - +
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Residues in contact with LEU 106 (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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97D GLU* 3.6 22.7 + - - +
100D THR* 3.8 12.3 - - + -
103D GLY* 3.6 14.3 - - - +
104D ALA 3.4 0.2 - - - -
105D LEU* 1.3 78.7 - - - +
107D ALA* 1.3 52.4 + - - +
109D LEU* 3.3 4.2 + - + -
110D SER* 2.8 37.4 + - - -
116D VAL* 3.6 24.0 - - + -
118D THR* 3.3 20.6 - - - +
133D LEU* 3.8 23.1 - - + -
142D VAL* 3.8 10.3 - - + -
144D PHE* 3.4 34.5 - - + -
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Residues in contact with ALA 107 (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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60D LEU* 4.3 2.7 - - + -
64D ILE* 4.2 11.0 - - + -
68D PHE* 3.9 22.2 - - + -
103D GLY 3.0 16.5 + - - +
104D ALA 3.9 6.5 - - - +
105D LEU 3.2 0.4 + - - -
106D LEU* 1.3 76.6 - - - +
108D VAL* 1.3 57.1 - - - +
110D SER* 3.7 3.0 + - - -
111D GLU* 3.2 32.9 + - - +
133D LEU* 4.0 11.9 - - + -
138D LEU* 3.9 17.0 - - + +
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Residues in contact with VAL 108 (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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85C LEU* 3.9 14.1 - - + -
60D LEU* 4.4 4.3 - - + -
64D ILE* 3.8 16.2 - - + -
80D SER* 3.4 45.5 - - - +
81D PHE* 3.9 22.0 - - + -
84D ALA* 3.8 11.7 - - + -
104D ALA 3.7 13.7 - - - +
105D LEU* 3.0 6.8 + - + +
107D ALA* 1.3 75.7 - - - +
109D LEU* 1.3 64.8 + - - +
110D SER 3.2 0.2 - - - -
111D GLU* 3.2 4.7 + - - +
112D VAL* 3.1 24.0 + - + +
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Residues in contact with LEU 109 (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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84D ALA* 4.3 14.4 - - - -
87D LEU* 4.3 15.0 - - + -
89D LEU* 3.9 24.9 - - + -
95D VAL* 4.3 16.2 - - + -
97D GLU* 3.8 37.7 - - + -
105D LEU* 3.0 35.2 + - + +
106D LEU* 3.7 6.7 - - - +
108D VAL* 1.3 76.2 - - - +
110D SER* 1.3 54.6 + - - +
112D VAL* 4.9 0.9 - - - -
113D ALA* 2.8 39.8 + - - +
116D VAL* 3.9 14.6 - - + -
163D PHE* 5.0 3.1 - - + -
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Residues in contact with SER 110 (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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91D LYS* 3.3 5.0 + - - -
106D LEU 2.8 22.2 + - - -
107D ALA* 3.7 8.1 - - - -
109D LEU* 1.3 74.4 - - - +
111D GLU* 1.3 64.6 + - - +
113D ALA 3.4 1.2 - - - +
116D VAL* 3.9 7.5 - - - +
133D LEU* 4.6 0.9 - - - -
138D LEU* 5.7 0.4 - - - -
139D GLY* 3.2 23.4 + - - -
140D LYS 4.3 0.2 + - - -
141D ASN* 2.6 48.5 + - - -
142D VAL* 3.8 13.5 - - - -
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Residues in contact with GLU 111 (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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85C LEU* 5.1 4.5 - - + -
89C LEU 4.6 3.5 - - - +
90C ASN* 2.9 46.5 + - + +
112C VAL* 5.7 2.1 - - - +
60D LEU* 4.2 22.8 - - + +
91D LYS* 3.0 21.2 + - - +
107D ALA 3.2 17.9 + - - +
108D VAL 3.2 5.6 + - - +
110D SER* 1.3 83.9 + - - +
112D VAL* 1.3 61.7 + - + +
137D ASN 5.4 0.2 - - - +
138D LEU* 3.7 29.0 - - + +
139D GLY 5.4 0.7 + - - -
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Residues in contact with VAL 112 (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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85C LEU* 3.9 28.9 - - + -
111C GLU 5.7 2.1 - - - +
112C VAL* 5.2 7.0 - - + +
84D ALA* 4.0 20.0 - - + +
85D LEU* 3.7 19.1 - - + -
89D LEU* 3.5 34.5 - - + +
90D ASN* 3.1 22.3 - - - -
91D LYS* 3.5 8.5 + - - +
108D VAL 3.1 17.3 + - - +
109D LEU* 4.3 1.3 - - - +
111D GLU* 1.3 81.4 - - - +
113D ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 113 (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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89D LEU* 3.8 23.8 - - + -
90D ASN 3.3 6.1 - - - -
91D LYS* 3.2 11.3 + - - -
93D LYS 3.7 9.9 - - - +
95D VAL* 3.8 17.7 - - + -
109D LEU 2.8 22.3 + - - +
112D VAL* 1.3 74.3 - - - +
114D GLY* 1.3 56.6 + - - +
115D GLU 4.3 3.4 - - - +
116D VAL* 4.4 1.8 - - + -
141D ASN* 2.8 27.4 + - - -
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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