Contacts of the helix formed by residues 97 - 114 (chain B) in PDB entry 2YF3
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 ASP 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 5.0 2.1 - - - +
27B GLU 5.7 0.2 + - - -
95B GLY 3.9 2.8 + - - -
96B ILE* 1.3 68.8 - - - +
98B ALA* 1.3 64.3 + - - +
99B ASP* 2.8 26.0 + - - +
100B ALA* 3.2 23.7 + - + +
101B VAL* 3.2 24.3 + - - +
141B LEU* 3.7 21.0 - - + +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 5.1 0.4 - - - -
81A ALA* 5.6 0.2 - - - +
84A LEU* 4.6 3.1 - - + +
11B ALA* 4.0 8.1 - - + +
88B TYR* 3.7 30.1 - - + +
91B LEU* 3.6 35.6 - - + +
92B ASP 5.7 0.2 - - - +
96B ILE 2.9 7.1 + - - +
97B ASP* 1.3 72.9 + - - +
99B ASP* 1.3 57.8 + - - +
101B VAL* 3.9 3.8 - - - +
102B PHE* 2.9 32.7 + - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 3.1 31.2 + - - +
13A ARG* 4.9 5.5 + - - +
9B THR* 2.6 40.5 + - - +
10B ASN 5.4 0.2 + - - -
11B ALA* 3.6 17.2 + - - +
12B GLU* 4.8 4.9 - - - +
88B TYR* 4.2 1.0 + - - -
97B ASP* 2.8 14.9 + - - +
98B ALA* 1.3 72.5 - - - +
100B ALA* 1.3 57.7 + - - +
102B PHE* 3.9 0.9 - - - +
103B ALA* 3.0 30.0 + - - +
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Residues in contact with ALA 100 (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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97B ASP* 3.2 28.7 + - + +
98B ALA 3.3 0.2 - - - -
99B ASP* 1.3 78.9 - - - +
101B VAL* 1.3 61.2 + - - +
103B ALA* 3.5 7.1 + - - +
104B GLU* 3.4 20.4 + - - +
137B VAL* 4.0 21.2 - - + +
141B LEU* 4.0 10.3 - - + -
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Residues in contact with VAL 101 (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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77A ALA* 3.8 11.4 - - + +
81A ALA* 3.6 23.6 - - + -
91B LEU* 5.0 3.1 - - + -
96B ILE* 3.4 32.8 - - + -
97B ASP 3.2 8.7 + - - +
98B ALA* 4.0 4.7 - - - +
100B ALA* 1.3 76.5 - - - +
102B PHE* 1.3 61.8 + - - +
104B GLU* 3.1 13.7 + - - +
105B VAL* 3.1 13.2 + - + +
134B VAL* 3.8 26.5 - - + -
137B VAL* 3.9 20.2 - - + -
138B ILE* 4.2 8.7 - - + -
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Residues in contact with PHE 102 (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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10A ASN* 3.2 47.3 - - + +
13A ARG* 4.0 16.2 - - + -
14A LEU* 3.5 16.2 - - + -
81A ALA* 4.2 10.4 - - + +
84A LEU* 3.8 26.0 - - + -
85A TYR* 3.4 52.7 - + - -
88A TYR* 4.0 8.1 - + - -
98B ALA 2.9 22.2 + - - +
99B ASP 3.9 3.4 - - - +
101B VAL* 1.3 72.5 - - - +
103B ALA* 1.3 54.9 + - - +
105B VAL* 3.2 5.6 + - + +
106B HIS* 2.7 32.8 + - + +
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Residues in contact with ALA 103 (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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13A ARG* 4.6 21.3 - - - +
99B ASP 3.0 19.2 + - - +
100B ALA* 3.7 8.1 - - - +
101B VAL 3.3 0.2 - - - -
102B PHE* 1.3 76.8 - - - +
104B GLU* 1.3 58.4 + - - +
106B HIS* 3.5 7.7 + - - +
107B ARG* 2.9 29.0 + - - +
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Residues in contact with GLU 104 (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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100B ALA 3.4 3.0 + - - +
101B VAL* 3.1 9.7 + - - +
103B ALA* 1.3 77.5 - - - +
105B VAL* 1.3 64.0 + - - +
107B ARG* 3.1 35.4 + - - +
108B ALA* 3.2 21.3 + - - +
130B ARG* 5.3 2.4 + - - -
132B ALA* 4.0 4.1 - - + +
133B ASP* 3.1 39.5 + - - +
134B VAL* 4.7 2.7 - - + +
137B VAL* 3.7 29.5 - - + +
140B ARG* 5.2 5.2 + - - -
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Residues in contact with VAL 105 (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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78A HIS* 4.1 21.8 - - + +
81A ALA* 3.9 22.0 - - + +
82A ASP* 3.6 18.4 - - - +
85A TYR* 4.1 13.5 - - + -
101B VAL 3.1 13.3 + - - +
102B PHE* 3.7 9.0 - - + +
104B GLU* 1.3 73.8 - - - +
106B HIS* 1.3 65.0 + - - +
108B ALA* 3.3 2.4 + - - +
109B ASN* 2.9 45.9 + - - +
132B ALA* 4.1 15.9 - - + -
134B VAL* 4.2 7.4 - - + -
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Residues in contact with HIS 106 (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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13A ARG* 3.3 58.5 - - + +
16A GLU* 2.9 27.1 + - - -
17A PHE* 4.3 4.7 - - + -
85A TYR* 2.8 39.6 + - + -
102B PHE* 2.7 21.4 + - + +
103B ALA 3.6 5.8 - - - +
105B VAL* 1.3 71.9 - - - +
107B ARG* 1.3 59.1 + - - +
109B ASN 3.2 0.2 + - - -
110B LEU* 2.8 50.3 + - + +
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Residues in contact with ARG 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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103B ALA 2.9 15.4 + - - +
104B GLU* 3.1 36.4 + - - +
105B VAL 3.2 0.6 - - - -
106B HIS* 1.3 79.2 - - - +
108B ALA* 1.3 72.9 + - - +
110B LEU* 3.6 5.1 + - - +
111B SER* 3.1 36.0 + - - -
130B ARG* 2.9 69.6 + - - +
131B PRO 3.1 18.8 + - - -
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Residues in contact with ALA 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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104B GLU 3.2 6.5 + - - +
105B VAL* 3.8 6.1 - - - +
107B ARG* 1.3 89.5 - - - +
109B ASN* 1.3 64.3 + - - +
111B SER* 4.3 0.2 - - - -
112B LYS* 3.0 12.0 + - - +
129B TRP* 2.8 34.2 + - + +
130B ARG 3.7 10.3 - - - +
131B PRO 4.0 0.2 - - - -
132B ALA* 3.6 31.6 - - + +
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Residues in contact with ASN 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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17A PHE* 3.5 21.2 - - + -
82A ASP* 5.3 1.8 + - - +
85A TYR* 3.3 44.5 - - - +
105B VAL* 2.9 33.5 + - - +
106B HIS 3.7 2.5 - - - +
108B ALA* 1.3 76.8 - - - +
110B LEU* 1.3 66.0 + - - +
112B LYS* 3.3 10.0 + - - +
113B ALA 3.1 18.0 + - - -
129B TRP* 5.8 1.4 - - - -
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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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16A GLU* 3.4 40.2 - - + +
17A PHE* 4.3 10.5 - - - -
20A ALA* 3.6 30.7 - - + +
106B HIS* 2.8 35.0 + - + +
107B ARG* 4.1 4.5 - - - +
109B ASN* 1.3 73.7 - - - +
111B SER* 1.3 63.4 + - - +
113B ALA* 3.2 19.0 + - - +
114B SER* 3.4 7.8 + - - -
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Residues in contact with SER 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 ARG* 3.1 27.5 + - - -
108B ALA* 3.6 6.3 - - - -
110B LEU* 1.3 75.2 - - - +
112B LYS* 1.3 62.7 + - - +
114B SER* 2.7 27.7 + - - -
126B PRO* 3.3 13.0 - - - +
129B TRP* 3.2 22.4 - - - -
130B ARG 4.8 0.9 + - - -
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Residues in contact with LYS 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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108B ALA 3.0 11.7 + - - +
109B ASN* 3.6 9.6 - - - +
111B SER* 1.3 75.1 - - - +
113B ALA* 1.3 57.5 - - - +
115B GLY 2.9 17.3 + - - -
122B LYS* 5.7 4.2 - - - +
123B GLN* 3.2 47.1 + - + +
124B LEU 3.3 4.0 - - - +
125B LYS* 4.1 34.4 - - + +
126B PRO* 3.9 3.8 - - - +
129B TRP* 3.3 24.5 - - + +
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Residues in contact with ALA 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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17A PHE* 4.2 3.8 - - + -
20A ALA* 4.0 27.5 - - + +
21A ILE* 3.6 27.6 - - + -
109B ASN 3.1 13.0 + - - +
110B LEU* 3.2 15.7 - - - +
111B SER 3.2 0.2 - - - -
112B LYS* 1.3 75.1 - - - +
114B SER* 1.3 59.7 + - - +
115B GLY 3.1 7.9 + - - +
123B GLN* 3.8 17.0 + - - +
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Residues in contact with SER 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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110B LEU 3.4 6.6 + - - -
111B SER* 2.7 22.7 + - - -
112B LYS 3.0 0.4 - - - -
113B ALA* 1.3 77.9 - - - +
115B GLY* 1.3 63.2 + - - +
126B PRO* 3.6 14.1 - - - +
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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
------------------------------------------------------------
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