Contacts of the helix formed by residues 124 - 137 (chain A) in PDB entry 2Y96
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 PHE 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A HIS* 6.1 0.7 - - - -
111A VAL* 3.7 46.7 - - + -
112A GLU* 4.9 8.5 - - + -
119A PHE* 3.7 27.6 - + - -
120A ASP 3.8 11.7 - - - -
121A LEU* 3.0 18.3 + - + +
122A SER 3.0 1.4 - - - -
123A VAL* 1.3 89.3 - - + +
125A PHE* 1.3 63.9 + - - +
126A TYR 3.4 1.6 - - - -
127A PRO* 3.6 5.1 - - + +
128A ALA* 3.0 26.8 + - - +
157A LEU* 4.6 6.3 - - + -
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.5 21.1 - - + -
122A SER* 3.1 35.6 + - - +
123A VAL 3.4 0.2 - - - -
124A PHE* 1.3 76.3 - - - +
126A TYR* 1.3 68.8 + + + +
128A ALA* 4.2 0.7 - - - +
129A ALA* 3.0 30.8 + - - +
156A THR* 3.7 24.5 - - + -
157A LEU* 4.1 11.5 - - + +
160A ALA* 3.9 20.0 - - + +
164A ILE* 4.0 4.2 - - + +
192A GLN* 3.9 29.4 - - + -
193A LEU* 4.0 15.3 - - + -
196A LEU* 3.7 28.9 - - + -
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 4.8 1.8 + - - -
123A VAL 4.8 0.6 + - - -
125A PHE* 1.3 84.1 - + + +
127A PRO* 1.4 67.4 - - + +
129A ALA* 3.2 3.5 + - - +
130A ALA* 2.8 29.4 + - - +
164A ILE* 3.5 44.0 - - + +
165A HIS* 4.8 3.1 + + - -
196A LEU* 3.7 19.2 - - + +
200A LEU* 3.5 26.9 - - - +
203A GLN* 5.2 2.3 + - - -
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Residues in contact with PRO 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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109A HIS* 4.2 14.6 - - + +
123A VAL 4.0 10.8 - - - +
124A PHE* 3.6 13.9 - - - +
126A TYR* 1.4 91.7 - - + +
128A ALA* 1.3 64.3 + - - +
130A ALA* 3.2 9.1 + - + +
131A PHE* 3.1 21.7 + - - +
1210A SO4 4.5 3.4 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.1 9.5 - - + +
109A HIS* 3.9 18.6 + - - +
111A VAL* 4.4 5.4 - - + -
124A PHE 3.0 20.6 + - - +
125A PHE 4.2 1.6 - - - +
127A PRO* 1.3 76.5 - - - +
129A ALA* 1.3 62.9 + - - +
131A PHE* 3.1 5.4 + - - +
132A ILE* 3.1 26.1 + - - +
157A LEU* 4.1 32.5 - - + +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE 3.0 21.3 + - - +
126A TYR* 3.6 3.8 - - - +
128A ALA* 1.3 77.3 - - - +
130A ALA* 1.3 57.5 + - - +
132A ILE* 3.3 6.7 + - - -
133A ASP* 2.9 29.5 + - - +
157A LEU 5.2 2.1 + - - +
161A TYR* 3.6 29.5 - - - +
164A ILE* 4.1 9.4 - - + -
165A HIS* 3.6 22.4 - - + +
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Residues in contact with ALA 130 (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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126A TYR 2.8 16.3 + - - +
127A PRO* 3.6 10.8 - - + +
128A ALA 3.2 0.4 - - - -
129A ALA* 1.3 76.1 - - - +
131A PHE* 1.3 57.8 + - - +
133A ASP* 3.4 4.4 + - - +
134A ARG* 2.9 49.9 + - + +
165A HIS* 4.0 12.1 + - + +
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Residues in contact with PHE 131 (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 HIS* 3.9 21.3 - + + -
84A VAL 4.1 8.5 - - - -
85A LEU* 4.1 12.3 - - + -
107A GLN* 3.6 33.9 - - + -
108A TYR 4.2 4.9 - - - -
109A HIS* 3.6 33.2 - + + +
127A PRO 3.1 11.7 + - - +
128A ALA 3.4 7.9 - - - +
130A ALA* 1.3 74.4 - - - +
132A ILE* 1.3 65.2 + - - +
134A ARG* 3.5 17.9 + - + +
135A ALA* 3.2 21.0 + - - +
143A ILE* 3.9 22.9 - - + -
1210A SO4 3.4 28.9 - - - +
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Residues in contact with ILE 132 (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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62A LEU* 3.9 13.7 - - + -
85A LEU* 3.8 23.1 - - + -
128A ALA 3.1 16.8 + - - +
129A ALA* 3.6 7.4 - - - +
131A PHE* 1.3 76.6 - - - +
133A ASP* 1.3 56.7 + - - +
135A ALA* 3.3 2.9 + - - +
136A LEU* 3.0 49.2 + - + +
143A ILE* 3.9 19.7 - - + -
145A VAL* 4.3 11.7 - - + -
157A LEU* 4.4 11.0 - - + +
158A VAL* 4.6 7.6 - - + -
161A TYR* 3.8 35.7 - - + -
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Residues in contact with ASP 133 (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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129A ALA 2.9 17.6 + - - +
130A ALA* 3.7 4.9 - - - +
132A ILE* 1.3 77.6 - - - +
134A ARG* 1.3 60.9 + - - +
136A LEU* 3.3 2.3 + - - +
137A SER* 3.0 31.1 + - - -
161A TYR* 3.7 23.0 + - + -
165A HIS* 3.6 34.3 + - + +
166A LYS* 4.9 6.2 + - - -
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Residues in contact with ARG 134 (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 HIS* 5.3 0.7 - - - -
130A ALA* 2.9 46.9 + - - +
131A PHE* 3.8 17.0 - - + +
132A ILE 3.4 0.4 - - - -
133A ASP* 1.3 74.1 - - + +
135A ALA* 1.3 65.7 + - - +
137A SER* 3.6 18.8 - - - -
138A ASP* 4.2 3.6 + - - +
1210A SO4 2.8 42.0 + - - -
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Residues in contact with ALA 135 (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 HIS* 3.6 45.9 + - + +
131A PHE 3.2 11.2 + - - +
132A ILE 3.5 8.1 - - - +
133A ASP 3.3 0.2 - - - -
134A ARG* 1.3 76.7 - - - +
136A LEU* 1.3 62.4 + - - +
138A ASP* 3.3 7.8 + - - +
141A SER* 2.7 28.4 + - - -
143A ILE* 4.2 18.2 - - + -
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Residues in contact with LEU 136 (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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59A TRP* 4.2 12.3 - - + +
60A PRO 3.8 5.4 - - - +
61A LYS* 3.6 39.7 - - + +
62A LEU* 4.1 15.7 - - + -
132A ILE* 3.0 34.5 + - + +
133A ASP* 3.3 4.0 + - - +
134A ARG 3.3 0.2 - - - -
135A ALA* 1.3 74.0 - - + +
137A SER* 1.3 62.7 + - - +
138A ASP 3.2 7.7 + - - +
139A ASP* 4.8 2.4 + - - +
141A SER 4.9 4.3 - - - +
143A ILE* 4.1 9.0 - - + -
161A TYR* 3.6 26.7 - - + +
166A LYS* 6.0 0.4 - - - +
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Residues in contact with SER 137 (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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133A ASP* 3.0 20.4 + - - -
134A ARG* 3.6 12.9 + - - -
136A LEU* 1.3 76.2 - - - +
138A ASP* 1.3 58.9 + - - +
139A ASP* 3.7 4.6 + - - +
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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