Contacts of the helix formed by residues 106 - 121 (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 HIS 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A HIS* 3.4 18.3 + + + +
103A ALA 3.1 13.0 + - - +
104A PRO 3.1 3.5 - - - -
105A SER* 1.3 83.1 + - - +
107A PRO* 1.3 85.4 - - + +
108A ASP* 2.9 53.4 + - + -
109A PHE* 3.0 34.1 + - + +
110A LEU* 3.3 4.3 + - - +
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Residues in contact with PRO 107 (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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104A PRO 5.5 0.4 - - - +
105A SER 4.8 0.2 - - - +
106A HIS* 1.3 100.6 - - + +
108A ASP* 1.3 57.8 + - - +
110A LEU* 3.3 16.1 + - + +
111A ASN* 2.8 32.2 + - - +
114A ARG* 5.3 1.7 + - - +
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Residues in contact with ASP 108 (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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49A HIS* 2.7 30.5 + - + +
53A LEU* 3.4 31.7 - - + +
106A HIS* 2.9 24.8 + - + -
107A PRO* 1.3 79.1 - - - +
109A PHE* 1.3 63.8 + - + +
111A ASN* 3.5 8.8 + - - +
112A ALA* 3.1 16.8 + - - -
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Residues in contact with PHE 109 (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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49A HIS* 3.6 35.4 - + - -
52A LEU* 3.8 28.3 - - + -
53A LEU* 3.7 31.6 - - + -
56A HIS* 3.7 34.9 - + + +
102A ASP* 4.2 5.4 - - - -
103A ALA* 3.3 18.2 - - - +
105A SER* 3.4 26.7 - - - -
106A HIS* 3.0 15.6 + - + -
108A ASP* 1.3 77.2 - - + +
110A LEU* 1.3 65.8 + - - +
112A ALA* 3.2 10.7 + - - +
113A TRP* 3.3 20.9 - - - -
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Residues in contact with LEU 110 (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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103A ALA* 3.7 12.5 + - + +
104A PRO* 3.8 41.3 - - + +
106A HIS 3.3 3.2 + - - +
107A PRO* 3.7 19.1 - - + +
109A PHE* 1.3 77.0 - - - +
111A ASN* 1.3 63.5 + - - +
113A TRP* 3.1 17.0 + - - +
114A ARG* 3.1 42.0 + - - +
154B ASP* 4.8 15.9 - - + +
2001B GOL 4.2 13.7 - - - +
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Residues in contact with ASN 111 (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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107A PRO 2.8 17.5 + - - +
108A ASP* 3.6 9.8 + - - +
110A LEU* 1.3 78.4 - - - +
112A ALA* 1.3 61.9 + - - +
114A ARG* 3.1 36.4 + - - +
115A THR* 4.1 5.0 + - - -
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Residues in contact with ALA 112 (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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53A LEU* 4.1 2.7 - - + -
56A HIS* 3.8 18.4 - - + -
57A GLU* 3.8 32.2 - - + +
60A ALA* 3.4 16.6 - - - +
108A ASP 3.1 12.9 + - - +
109A PHE 3.4 11.9 - - - +
110A LEU 3.2 0.2 - - - -
111A ASN* 1.3 78.6 - - - +
113A TRP* 1.3 59.4 + - + +
115A THR* 4.7 4.5 + - - -
116A VAL* 5.0 1.2 + - - +
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Residues in contact with TRP 113 (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* 3.0 37.7 + - + +
59A LEU* 3.8 19.1 - - + -
60A ALA* 3.7 30.3 - - + -
63A TRP* 4.3 3.8 - + - -
96A GLU* 3.7 21.5 - - + -
99A LEU* 5.7 0.7 - - + -
100A LEU* 3.7 25.7 - - + +
103A ALA* 4.3 11.8 - - + +
109A PHE 3.3 22.4 - - - -
110A LEU 3.1 8.1 + - - +
112A ALA* 1.3 79.4 - - - +
114A ARG* 1.3 62.4 + - - +
115A THR 3.5 1.1 - - - -
116A VAL* 3.2 14.5 - - + +
117A ASN* 3.0 34.8 + - - -
1001A MBT 3.4 31.0 - + - -
154B ASP* 4.5 1.8 - - + +
2001B GOL 3.7 21.8 - - - -
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Residues in contact with ARG 114 (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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107A PRO* 5.3 1.6 + - - +
110A LEU* 3.1 49.3 + - - +
111A ASN* 3.1 31.7 + - - +
113A TRP* 1.3 77.1 - - - +
115A THR* 1.3 59.0 + - - +
117A ASN* 3.4 0.3 + - - -
118A HIS* 2.8 64.8 + - + +
154B ASP* 4.0 30.1 + - - +
155B ASP* 5.6 0.8 + - - -
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Residues in contact with THR 115 (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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64A ASP* 6.3 0.7 - - - -
111A ASN 4.1 4.7 + - - -
112A ALA 4.7 3.5 + - - -
113A TRP 3.5 0.6 - - - -
114A ARG* 1.3 78.6 - - - +
116A VAL* 1.3 65.4 + - - +
118A HIS* 3.2 5.2 + - - +
119A GLN* 3.0 48.7 + - + +
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Residues in contact with VAL 116 (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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60A ALA* 4.1 17.0 - - + +
63A TRP* 3.7 35.0 - - + -
64A ASP* 3.8 29.6 - - + +
67A LEU* 4.4 0.4 - - + -
112A ALA 5.2 1.0 + - - -
113A TRP* 3.2 28.4 - - + +
115A THR* 1.3 81.2 - - - +
117A ASN* 1.3 65.9 + - - +
119A GLN* 4.6 2.0 - - - -
120A TRP* 3.1 47.7 + - + +
121A ILE* 4.9 0.2 - - - +
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Residues in contact with ASN 117 (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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63A TRP* 4.2 10.5 - - - -
113A TRP* 3.0 24.5 + - - +
114A ARG 3.9 1.6 - - - +
116A VAL* 1.3 87.0 - - - +
118A HIS* 1.3 63.3 + - - +
121A ILE* 2.9 60.3 + - + +
1001A MBT 5.3 0.5 - - - -
152B ILE 4.9 0.9 - - - +
153B HIS* 4.6 7.4 + - - -
154B ASP* 3.5 26.3 + - - +
2001B GOL 3.0 30.9 + - - -
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Residues in contact with HIS 118 (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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114A ARG* 2.8 56.1 + - + +
115A THR* 3.8 6.1 - - - +
117A ASN* 1.3 80.6 - - - +
119A GLN* 1.3 63.4 + - + +
121A ILE 4.5 5.5 - - - +
154B ASP* 4.4 13.9 - - - -
155B ASP* 4.9 6.3 - - - -
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Residues in contact with GLN 119 (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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64A ASP* 3.8 18.4 - - - +
80A ARG* 3.4 26.7 + - - -
115A THR* 3.0 38.5 + - + +
118A HIS* 1.3 82.8 - - + +
120A TRP* 1.3 72.3 + - + +
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Residues in contact with TRP 120 (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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63A TRP* 5.5 0.4 - - + -
64A ASP* 3.0 19.0 + - - -
67A LEU* 3.5 54.1 - - + +
68A ARG* 3.8 23.6 - - + -
71A THR* 3.3 33.7 - - + -
74A PRO* 4.4 10.8 - - + -
80A ARG* 3.8 49.8 + - + +
81A LEU* 5.2 1.7 + - - -
84A VAL* 3.5 20.0 - - + +
116A VAL* 3.1 31.2 + - + +
119A GLN* 1.3 94.0 + - + +
121A ILE* 1.3 66.2 + - + +
122A PRO* 4.1 3.8 - - - +
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Residues in contact with ILE 121 (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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63A TRP* 3.6 28.5 - - + -
84A VAL* 3.7 28.0 - - + -
117A ASN* 2.9 42.5 + - + +
118A HIS* 4.5 6.1 - - - +
120A TRP* 1.3 82.9 - - + +
122A PRO* 1.3 82.8 - - + +
123A ASP* 3.5 2.3 + - - +
140A GLN* 3.8 11.4 - - + +
1001A MBT 5.9 0.7 - - - -
153B HIS* 3.6 33.0 - - + +
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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