Contacts of the helix formed by residues 109 - 127 (chain A) in PDB entry 2Y8P
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 ASN 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A SER 3.5 4.9 + - - +
106A GLU* 3.1 15.7 + - - +
108A LYS* 1.3 77.1 - - - +
110A PRO* 1.3 69.4 - - - +
111A GLU* 3.1 12.1 + - - +
112A ARG* 2.9 45.2 + - + +
113A ASN* 2.9 29.9 + - - +
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Residues in contact with PRO 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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39A TRP* 3.6 43.5 - - + -
42A ILE* 4.4 5.8 - - + -
69A PRO* 4.1 11.4 - - + -
80A LEU* 3.8 14.8 - - + -
108A LYS 3.2 10.5 - - - +
109A ASN* 1.3 90.7 - - - +
111A GLU* 1.3 62.6 + - - +
113A ASN* 4.2 3.4 - - + -
114A ILE* 3.0 30.1 + - - +
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Residues in contact with GLU 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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42A ILE* 4.0 29.3 - - + +
109A ASN* 3.1 11.5 + - - +
110A PRO* 1.3 79.7 - - - +
112A ARG* 1.3 68.0 + - - +
114A ILE* 4.1 1.4 - - - +
115A SER* 3.1 22.7 + - - -
97B GLY 4.4 5.1 - - - +
98B TRP* 3.9 22.3 - - + +
99B SER* 3.0 46.3 + - - +
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Residues in contact with ARG 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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93A TYR* 5.5 2.6 + - - -
106A GLU* 3.7 50.9 + - + +
107A LEU* 5.7 0.2 - - - -
109A ASN* 2.9 24.4 + - - +
111A GLU* 1.3 78.0 - - + +
113A ASN* 1.3 66.1 - - - +
115A SER* 3.3 5.6 + - - -
116A MET* 3.0 36.6 + - + +
98B TRP* 6.0 0.9 - - - +
106B GLU* 5.4 5.9 + - - -
112B ARG* 4.5 19.8 - - - +
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Residues in contact with ASN 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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78A ILE 3.0 19.6 - - - +
79A GLY* 3.6 0.2 - - - -
80A LEU* 3.2 16.0 - - + +
81A MET* 2.7 39.0 - - - +
83A LEU* 3.6 12.7 - - - +
106A GLU 4.6 0.2 + - - -
107A LEU* 2.8 30.3 + - - +
108A LYS 5.2 0.4 - - - +
109A ASN 2.9 17.5 + - - +
110A PRO* 3.7 8.1 - - + +
112A ARG* 1.3 76.3 - - - +
114A ILE* 1.3 57.8 + - - +
116A MET* 3.2 4.6 + - - -
117A GLY* 2.9 23.7 + - - -
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 3.8 20.6 - - + -
42A ILE* 3.6 27.6 - - + -
43A SER* 4.0 10.3 - - - +
46A ALA* 3.8 19.1 - - + -
57A ILE* 3.9 21.1 - - + -
61A ILE* 4.0 11.9 - - + -
80A LEU* 3.7 27.1 - - + -
81A MET* 3.8 9.6 - - - +
110A PRO 3.0 18.7 + - - +
113A ASN* 1.3 72.6 - - - +
115A SER* 1.3 67.3 + - - +
117A GLY* 3.3 1.0 + - - -
118A ALA* 3.0 22.3 + - - +
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Residues in contact with SER 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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42A ILE* 5.3 0.2 - - - +
46A ALA* 4.2 14.8 - - - +
50A TRP* 3.9 11.0 + - - -
111A GLU* 3.1 20.7 + - - -
112A ARG* 3.6 7.0 - - - -
114A ILE* 1.3 77.8 - - - +
116A MET* 1.3 60.0 + - - +
118A ALA* 3.5 2.8 + - - +
119A ALA* 3.0 27.2 + - - +
96B MET 4.2 5.4 + - - -
98B TRP* 3.0 35.3 + - - -
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Residues in contact with MET 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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83A LEU* 3.5 15.9 - - + +
89A GLY* 3.6 38.4 - - - +
92A VAL* 3.6 22.9 - - + +
93A TYR* 3.9 16.6 - - + -
98A TRP* 6.3 1.3 - - + -
102A PRO* 3.8 15.9 - - + -
106A GLU* 6.4 0.2 - - - -
107A LEU* 4.0 20.0 - - + -
112A ARG* 3.0 27.3 + - - +
113A ASN* 3.2 3.1 + - - +
115A SER* 1.3 76.7 - - - +
117A GLY* 1.3 59.3 + - - +
119A ALA* 3.3 7.9 + - - +
120A TYR* 2.8 30.3 + - - +
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Residues in contact with GLY 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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81A MET* 3.6 28.8 - - - +
83A LEU* 3.9 12.9 - - - +
113A ASN 2.9 11.8 + - - -
114A ILE 3.3 0.4 + - - -
116A MET* 1.3 76.3 - - - +
118A ALA* 1.3 56.9 + - - +
120A TYR* 3.4 3.7 + - - +
121A LEU* 3.0 32.7 + - - +
146A TYR* 4.3 5.2 - - - -
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Residues in contact with ALA 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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46A ALA* 3.9 26.9 - - + +
50A TRP* 4.1 7.2 - - + -
52A VAL* 3.6 13.3 - - + +
57A ILE* 4.0 20.4 - - + -
81A MET* 4.3 0.8 - - - +
114A ILE 3.0 17.1 + - - +
115A SER 3.7 4.3 - - - +
117A GLY* 1.3 74.5 - - - +
119A ALA* 1.3 65.6 + - - +
121A LEU* 3.2 9.5 + - - -
122A ASN* 3.0 18.9 + - - +
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Residues in contact with ALA 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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50A TRP* 3.4 42.4 - - + +
92A VAL* 3.8 22.7 - - + -
115A SER 3.0 15.8 + - - +
116A MET 3.6 4.9 - - - +
118A ALA* 1.3 77.2 - - - +
120A TYR* 1.3 56.4 + - - +
122A ASN* 3.1 4.9 + - - +
123A ILE* 3.0 33.7 + - + +
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Residues in contact with TYR 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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83A LEU* 4.9 4.3 - - + -
88A SER* 3.6 40.1 - - - -
91A ASP* 3.8 27.4 + - + -
92A VAL* 3.9 8.7 - - + +
116A MET 2.8 21.0 + - - +
117A GLY* 3.7 7.2 - - - +
118A ALA 3.2 0.2 - - - -
119A ALA* 1.3 73.4 - - - +
121A LEU* 1.3 60.3 + - - +
123A ILE* 3.3 10.0 + - + +
124A LEU* 3.0 59.5 + - + +
145A SER 5.4 2.2 + - - -
146A TYR* 3.7 36.1 - + + -
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Residues in contact with LEU 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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52A VAL* 4.2 28.5 - - + -
56A LEU* 4.5 8.7 - - + -
57A ILE* 4.4 6.3 - - + -
60A ILE* 3.6 28.5 - - + -
81A MET* 4.0 13.5 - - + -
117A GLY 3.0 21.1 + - - +
118A ALA 3.2 6.0 + - - +
120A TYR* 1.3 75.2 - - - +
122A ASN* 1.3 58.5 + - - +
124A LEU* 3.6 7.1 + - + +
125A GLU* 3.0 29.0 + - - +
142A LEU* 3.7 32.2 - - + +
146A TYR* 3.6 27.1 - - + -
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Residues in contact with ASN 122 (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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50A TRP* 2.9 58.2 + - + +
51A GLY 5.3 1.0 + - - -
52A VAL* 4.1 4.2 - - + +
95A ARG* 4.8 8.0 + - - -
118A ALA 3.0 9.3 + - - +
119A ALA 3.5 7.6 - - - +
121A LEU* 1.3 73.8 - - - +
123A ILE* 1.3 59.2 + - - +
125A GLU* 3.7 8.4 + - - -
126A THR* 2.8 59.3 + - - +
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Residues in contact with ILE 123 (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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50A TRP* 5.5 0.4 - - + -
91A ASP* 3.7 24.7 - - + +
92A VAL* 4.0 15.9 - - + +
95A ARG* 3.5 42.4 - - + -
119A ALA* 3.0 18.6 + - + +
120A TYR* 3.3 15.7 + - + +
122A ASN* 1.3 77.3 - - - +
124A LEU* 1.3 65.3 + - + +
126A THR* 3.6 6.1 + - - -
127A GLY* 2.8 31.4 + - - -
128A PRO* 3.6 4.3 - - + +
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Residues in contact with LEU 124 (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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120A TYR* 3.0 56.8 + - + +
121A LEU* 3.7 9.0 - - + +
123A ILE* 1.3 82.6 - - + +
125A GLU* 1.3 62.1 + - - +
127A GLY 3.4 1.2 + - - -
128A PRO* 3.5 15.4 - - + +
129A LEU* 3.1 33.3 + - + +
142A LEU* 3.7 17.9 - - + +
145A SER* 4.2 12.6 - - - -
146A TYR* 4.0 30.5 - - + +
150A ALA* 5.1 2.5 - - + -
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Residues in contact with GLU 125 (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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51A GLY 4.2 15.1 - - - +
52A VAL* 5.2 3.6 - - - +
121A LEU 3.0 18.9 + - - +
122A ASN* 3.2 10.1 + - - +
124A LEU* 1.3 76.7 - - - +
126A THR* 1.3 67.0 + - + +
129A LEU* 3.6 7.1 - - - +
130A ALA* 3.2 26.2 + - - -
138A LEU* 4.0 29.5 - - + +
142A LEU* 3.9 19.5 - - + +
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Residues in contact with THR 126 (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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95A ARG* 5.8 1.0 + - - -
122A ASN* 2.8 50.4 + - - +
123A ILE* 3.6 5.5 + - - -
125A GLU* 1.3 81.2 - - + +
127A GLY* 1.3 62.9 + - - +
130A ALA* 3.6 12.6 - - - +
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Residues in contact with GLY 127 (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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123A ILE 2.8 11.4 + - - -
125A GLU 3.3 1.0 - - - -
126A THR* 1.3 78.6 - - - +
128A PRO* 1.3 73.9 - - - +
129A LEU 3.1 2.2 + - - -
130A ALA* 3.1 17.0 + - - +
161A ARG* 5.3 3.2 - - - -
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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