Contacts of the helix formed by residues 93 - 103 (chain A) in PDB entry 2YVE
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 SER 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ILE* 5.7 1.7 - - - +
91A ASN 3.7 1.4 + - - -
92A VAL* 1.3 82.0 - - - +
94A ARG* 1.3 64.3 + - - +
95A PRO* 3.5 11.1 - - - +
96A GLU* 3.1 24.5 + - - +
97A LEU* 3.0 20.6 + - - +
151A TYR* 3.9 3.1 - - - -
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Residues in contact with ARG 94 (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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17A ILE 2.9 23.4 + - - -
18A GLY* 3.4 19.3 + - - +
20A TYR 2.9 22.0 + - - -
21A SER* 3.9 9.1 - - - +
93A SER* 1.3 71.9 - - - +
95A PRO* 1.3 72.1 - - + +
97A LEU* 3.2 4.9 + - - +
98A LEU* 2.9 47.5 + - + +
151A TYR* 3.4 30.5 + - + +
23B GLU* 4.5 6.3 + - - -
101B ILE* 3.8 32.5 + - + +
102B ASP* 4.8 14.0 + - - +
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Residues in contact with PRO 95 (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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14A ILE* 3.5 33.0 - - + +
15A ASP* 5.4 0.7 - - - -
17A ILE* 3.9 19.5 - - + +
18A GLY* 3.3 33.2 - - - +
59A LEU* 5.4 0.2 - - - -
93A SER* 3.5 11.7 - - - +
94A ARG* 1.3 94.1 - - + +
96A GLU* 1.3 60.8 + - - +
98A LEU* 3.3 2.6 + - + +
99A LEU* 2.9 30.5 + - - +
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Residues in contact with GLU 96 (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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14A ILE* 5.4 0.8 - - + +
59A LEU* 3.4 49.2 - - + +
92A VAL* 3.9 21.2 - - + +
93A SER* 3.1 21.2 + - - +
95A PRO* 1.3 77.3 - - - +
97A LEU* 1.3 57.7 + - - +
99A LEU* 3.2 2.9 + - - +
100A LEU* 2.8 38.1 + - + +
113A TRP* 3.7 2.4 - - + -
147A PHE* 4.0 2.9 - - - -
1001A MBT 3.2 45.4 + - - -
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Residues in contact with LEU 97 (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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92A VAL* 3.8 23.2 - - + +
93A SER 3.0 17.2 + - - +
94A ARG* 3.2 4.7 + - - +
96A GLU* 1.3 77.9 - - - +
98A LEU* 1.3 60.7 + - - +
100A LEU* 3.2 6.3 + - + +
101A ILE* 3.0 38.2 + - + +
148A VAL* 4.6 11.2 - - + -
151A TYR* 3.9 20.2 - - + -
152A ILE* 6.2 1.1 - - + -
97B LEU* 5.2 6.7 - - + -
101B ILE* 3.6 37.2 - - + -
151B TYR* 5.8 0.4 - - + -
152B ILE* 3.9 28.0 - - + -
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Residues in contact with LEU 98 (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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17A ILE* 4.1 18.8 - - + -
21A SER* 5.4 0.4 - - - -
22A LEU* 4.1 19.0 - - + +
94A ARG* 2.9 60.2 + - + +
95A PRO* 3.8 3.8 - - + +
97A LEU* 1.3 76.1 - - - +
99A LEU* 1.3 62.6 + - - +
101A ILE* 3.4 6.8 + - + +
102A ASP* 3.0 23.6 + - - +
98B LEU* 4.2 25.1 - - + -
101B ILE* 4.2 20.4 - - + -
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Residues in contact with LEU 99 (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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14A ILE* 4.6 4.9 - - + -
17A ILE* 4.3 17.0 - - + -
22A LEU* 4.1 27.6 - - + -
52A LEU* 4.4 11.2 - - + -
55A MET* 4.3 21.3 - - + -
56A HIS* 3.1 37.3 - - + +
59A LEU* 3.6 27.4 - - + -
95A PRO* 2.9 22.3 + - + +
96A GLU* 3.2 5.1 + - - +
98A LEU* 1.3 75.3 - - + +
100A LEU* 1.3 65.5 + - - +
102A ASP* 3.1 4.4 + - + +
103A ALA 2.9 19.6 + - - -
113A TRP* 5.7 1.6 - - + -
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Residues in contact with LEU 100 (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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56A HIS* 5.1 0.2 - - - -
96A GLU* 2.8 33.3 + - + +
97A LEU* 3.2 12.3 + - + +
99A LEU* 1.3 74.4 - - - +
101A ILE* 1.3 64.8 + - - +
103A ALA* 3.3 5.7 + - - -
104A PRO* 3.7 0.9 - - - +
113A TRP* 3.7 33.4 - - + +
147A PHE* 4.3 8.7 - - + -
1001A MBT 3.7 30.7 - - - +
151B TYR 3.5 8.0 - - - +
152B ILE* 4.0 19.7 - - + -
2001B GOL 2.8 49.1 + - - +
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Residues in contact with ILE 101 (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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97A LEU* 3.0 27.8 + - + +
98A LEU* 3.6 9.4 - - + +
100A LEU* 1.3 77.6 - - - +
102A ASP* 1.3 59.0 + - + +
104A PRO* 3.3 15.9 - - - +
94B ARG* 3.8 29.2 + - + +
97B LEU* 3.5 25.6 - - + -
98B LEU* 4.6 15.7 - - + -
101B ILE* 3.4 33.2 - - + -
151B TYR* 4.0 30.5 - - + +
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Residues in contact with ASP 102 (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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22A LEU* 3.9 23.6 - - + +
52A LEU* 4.8 10.9 - - - +
56A HIS* 4.8 5.7 + - - +
98A LEU 3.0 16.9 + - - +
99A LEU* 3.1 5.9 + - - +
101A ILE* 1.3 78.5 - - + +
103A ALA* 1.3 59.2 + - - +
104A PRO* 3.3 1.8 - - - -
105A SER* 2.8 49.3 + - - -
109A PHE* 4.2 7.6 - - - -
94B ARG* 5.1 10.1 + - - +
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Residues in contact with ALA 103 (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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56A HIS* 3.8 19.1 - - + +
99A LEU 2.9 7.1 + - - +
100A LEU 3.3 2.6 + - - +
102A ASP* 1.3 75.9 - - - +
104A PRO* 1.3 59.4 - - - +
105A SER 2.9 5.7 + - - -
106A HIS 3.1 19.9 + - - +
109A PHE* 3.3 20.2 - - + +
110A LEU* 3.7 8.3 - - + +
113A TRP* 4.3 6.1 - - + +
2001B GOL 3.4 32.1 - - - +
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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