Contacts of the helix formed by residues 106 - 121 (chain B) 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 HIS 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B HIS* 3.6 23.2 + + - -
103B ALA 3.1 12.8 + - - +
104B PRO 3.1 2.0 - - - -
105B SER* 1.3 83.4 + - - +
107B PRO* 1.4 84.5 - - + +
108B ASP* 3.0 39.1 + - + +
109B PHE* 3.0 34.2 + + + -
110B LEU* 3.2 7.6 + - - +
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Residues in contact with PRO 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PRO 5.8 0.2 - - - +
105B SER 4.8 0.7 - - - +
106B HIS* 1.4 99.0 - - + +
108B ASP* 1.3 57.1 + - - +
110B LEU* 3.7 13.9 - - + +
111B ASN* 2.8 30.7 + - - +
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B HIS* 2.8 28.3 + - + +
53B LEU* 3.4 34.4 - - + +
106B HIS* 3.0 22.2 + - + +
107B PRO* 1.3 79.3 - - - +
109B PHE* 1.3 63.2 + - - +
111B ASN* 3.4 12.1 + - - +
112B ALA 3.1 16.5 + - - -
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B HIS* 3.5 35.0 - + - -
52B LEU* 3.8 27.8 - - + -
53B LEU* 3.8 31.0 - - + -
56B HIS* 3.7 32.3 - + + +
102B ASP* 4.2 7.2 - - - -
103B ALA* 3.4 17.5 - - + +
105B SER* 3.6 22.2 - - - -
106B HIS* 3.0 20.2 + + + -
108B ASP* 1.3 76.4 - - - +
110B LEU* 1.3 66.0 + - - +
112B ALA* 3.1 16.5 + - - +
113B TRP* 3.4 13.3 - - - -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS 4.7 1.8 - - - +
154A ASP* 3.5 42.1 - - + +
103B ALA* 3.7 10.5 - - + -
104B PRO* 3.7 51.6 - - + +
106B HIS 3.2 11.9 + - - +
107B PRO* 3.7 14.1 - - + +
109B PHE* 1.3 78.4 - - - +
111B ASN* 1.3 59.0 + - - +
113B TRP* 3.1 7.6 + - + +
114B ARG* 2.9 25.6 + - - +
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PRO 2.8 18.7 + - - +
108B ASP* 3.6 14.0 + - - +
109B PHE 3.2 0.2 - - - -
110B LEU* 1.3 79.4 - - - +
112B ALA* 1.3 62.3 + - - +
114B ARG* 3.2 27.0 + - - +
115B THR* 4.0 6.2 + - - -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.9 13.5 - - + -
56B HIS* 3.8 18.8 - - + -
57B GLU* 3.7 31.6 - - + +
60B ALA* 3.6 16.7 - - - +
108B ASP 3.1 6.5 + - - -
109B PHE 3.1 10.7 + - - +
111B ASN* 1.3 77.8 - - - +
113B TRP* 1.3 59.3 + - - +
115B THR* 4.5 5.2 + - - -
116B VAL 5.2 0.9 + - - -
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 4.2 9.6 - - + +
56B HIS* 2.9 38.7 + - + +
59B LEU* 3.7 37.9 - - + -
60B ALA* 3.7 24.5 - - + -
63B TRP* 4.4 3.1 - + - -
96B GLU* 3.8 5.6 - - + -
99B LEU* 5.4 2.5 - - + -
100B LEU* 3.6 27.8 - - + +
103B ALA* 4.1 12.3 - - + +
109B PHE 3.4 20.3 + - - -
110B LEU* 3.1 7.9 + - - +
112B ALA* 1.3 76.1 - - - +
114B ARG* 1.3 65.0 + - - +
115B THR 3.4 1.6 - - - -
116B VAL* 3.3 13.1 - - + +
117B ASN* 3.0 35.1 + - - +
1002B MBT 3.3 41.7 - + - -
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 3.3 26.7 - - - +
110B LEU 2.9 10.0 + - - +
111B ASN* 3.2 26.8 + - - +
113B TRP* 1.3 77.9 - - - +
115B THR* 1.3 63.7 + - - +
117B ASN* 5.7 0.2 - - + -
118B HIS* 2.7 77.6 + - + +
2006B GOL 5.7 5.8 + - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASN 4.0 6.4 + - - -
112B ALA 4.5 3.9 + - - -
113B TRP 3.4 0.8 - - - -
114B ARG* 1.3 82.3 + - - +
116B VAL* 1.3 65.9 + - - +
118B HIS* 3.7 5.6 - - + +
119B GLN* 2.9 40.0 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ALA* 3.9 28.0 - - + +
63B TRP* 3.6 36.4 - - + -
64B ASP* 3.9 30.5 - - + +
67B LEU* 4.2 0.2 - - + -
112B ALA 5.2 1.2 + - - -
113B TRP* 3.3 17.2 - - + +
115B THR* 1.3 80.3 - - - +
117B ASN* 1.3 67.1 + - - +
119B GLN* 4.7 0.9 - - - -
120B TRP* 3.1 41.6 + - + +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS* 3.1 30.6 + - - +
154A ASP* 3.0 31.1 + - - +
63B TRP* 4.3 11.0 - - - -
113B TRP* 3.0 41.8 + - - +
114B ARG* 3.7 2.2 - - + +
116B VAL* 1.3 84.8 - - - +
118B HIS* 1.3 56.7 + - - +
121B ILE* 2.8 33.8 + - - +
1002B MBT 4.8 4.0 - - - -
2006B GOL 2.4 26.7 + - - -
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ARG* 2.7 66.5 + - - +
115B THR* 3.7 4.3 - - + +
117B ASN* 1.3 75.7 - - - +
119B GLN* 1.3 85.9 + - - +
120B TRP 3.7 0.3 + - - -
121B ILE 4.4 5.0 - - - +
123B ASP* 5.6 3.6 - - - -
2006B GOL 3.6 23.9 + - - +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASP* 5.3 1.6 - - - +
80B ARG* 2.9 32.7 + - - +
115B THR* 2.9 34.9 + - + +
116B VAL* 4.7 0.9 - - - -
118B HIS* 1.3 101.1 + - - +
120B TRP* 1.3 75.5 + - + +
121B ILE 5.3 0.2 - - - -
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Residues in contact with TRP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TRP* 5.3 2.0 - - + -
64B ASP* 3.0 19.8 + - - -
67B LEU* 3.5 50.5 - - + +
68B ARG* 3.9 23.8 - - + -
71B THR* 3.3 30.1 - - - -
74B PRO* 5.5 2.0 - - + -
80B ARG* 3.4 68.6 - - + +
81B LEU* 5.5 1.7 - - - -
84B VAL* 3.6 24.2 - - + +
116B VAL* 3.1 30.8 + - + +
119B GLN* 1.3 86.8 - - + +
121B ILE* 1.3 68.3 + - + +
122B PRO* 3.7 4.9 - - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS* 3.9 12.6 - - + +
155A ASP* 6.0 0.7 - - - +
63B TRP* 3.8 24.0 - - + -
84B VAL* 4.2 8.1 - - + -
117B ASN* 2.8 39.6 + - - +
118B HIS 4.4 5.7 - - - +
119B GLN 5.3 0.2 - - - -
120B TRP* 1.3 72.8 - - - +
122B PRO* 1.3 86.0 - - + +
123B ASP* 3.4 2.6 + - - -
137B TYR* 4.2 9.4 - - + +
140B GLN* 3.3 39.3 - - + +
2006B GOL 3.0 26.5 + - - +
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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