Contacts of the helix formed by residues 121 - 135 (chain A) in PDB entry 2I91
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 ILE 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A CYS 4.4 0.7 - - - -
120A ARG* 1.3 84.9 - - + +
122A PRO* 1.3 77.9 - - + +
123A THR* 3.9 8.7 - - - +
124A HIS* 2.9 47.3 + - + +
125A LEU 3.5 2.6 + - - -
155A TRP* 3.9 5.6 - - - -
171A TYR* 4.0 19.7 - - + +
12D U 3.9 25.4 - - - +
13D C 4.0 30.7 - - - +
14D A 3.8 21.5 - - - +
15D A 6.0 1.3 - - - +
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Residues in contact with PRO 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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120A ARG 4.7 0.2 - - - +
121A ILE* 1.3 86.0 - - + +
123A THR* 1.3 61.8 + - - +
125A LEU* 2.9 8.5 + - + +
126A PHE* 2.8 38.7 + - + -
155A TRP* 3.7 23.9 - - + -
167A ALA* 3.8 25.6 - - + +
171A TYR* 3.7 22.7 - - + -
179A HIS* 3.3 31.0 - - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.0 8.0 + - - -
122A PRO* 1.3 75.9 - - - +
124A HIS* 1.3 61.2 + - + +
126A PHE* 3.2 11.8 + - - +
127A THR* 2.8 44.3 + - - +
171A TYR* 3.4 17.8 - - - -
174A ARG* 3.5 18.2 - - + +
175A ASN* 4.3 7.9 - - - +
11D U 4.6 8.7 - - + -
12D U 2.7 28.0 + - - +
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Residues in contact with HIS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 3.2 46.0 + - + +
93A LEU* 3.2 21.8 - - + +
118A VAL 3.7 5.5 + - - +
119A CYS* 3.5 18.4 - - - -
120A ARG* 3.2 26.2 + - - -
121A ILE* 2.9 32.1 + - + +
123A THR* 1.3 79.9 - - + +
125A LEU* 1.3 57.2 + - - +
128A PHE* 3.0 24.8 + - - +
13D C 3.4 28.8 - + - -
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Residues in contact with LEU 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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115A VAL* 4.6 12.1 - - + -
119A CYS* 4.0 8.0 - - + +
121A ILE 3.5 2.4 + - - +
122A PRO* 2.9 12.2 + - + +
124A HIS* 1.3 78.8 - - - +
126A PHE* 1.3 61.9 + - + +
128A PHE* 2.9 19.1 + - + +
129A ILE* 2.8 55.8 + - + +
152A VAL* 4.6 10.8 - - + -
155A TRP* 3.8 49.1 - - + +
156A TYR* 4.6 4.7 - - + +
179A HIS* 6.2 0.4 - - + -
182A LEU* 3.8 24.0 - - + -
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Residues in contact with PHE 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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122A PRO* 2.8 36.5 + - + -
123A THR* 3.6 5.2 - - - +
125A LEU* 1.3 72.7 - - + +
127A THR* 1.3 57.7 + - - +
129A ILE* 3.4 4.2 + - - +
130A GLN* 3.0 30.5 + - - +
171A TYR 4.3 1.8 - - - -
173A GLN* 4.0 5.8 - - - -
174A ARG* 3.6 42.4 - - + +
175A ASN* 4.4 5.8 - - - +
177A TRP* 3.5 36.8 - - + -
178A SER* 3.8 17.5 - - - -
179A HIS* 3.5 30.5 - + - -
182A LEU* 3.4 30.7 - - + -
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 4.2 18.5 + - + +
93A LEU* 3.7 21.3 - - + -
123A THR* 2.8 21.4 + - - +
126A PHE* 1.3 76.1 - - - +
128A PHE* 1.3 61.8 + - - +
130A GLN* 3.7 5.8 + - - +
131A PHE* 3.2 48.7 + - + -
175A ASN* 3.1 21.9 + - - -
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Residues in contact with PHE 128 (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 LEU* 3.8 26.0 - - + -
96A LEU* 3.2 44.4 - - + -
97A ALA* 3.6 9.9 - - + -
100A SER* 4.0 9.9 - - - -
112A PHE* 4.5 5.6 - + - -
115A VAL* 4.0 17.9 - - + -
119A CYS* 4.3 8.3 - - - -
124A HIS 3.0 14.9 + - - +
125A LEU* 2.9 26.1 + - + +
127A THR* 1.3 74.9 - - - +
129A ILE* 1.3 69.5 + - + +
131A PHE* 3.1 8.4 + - - +
132A LYS* 3.1 47.3 + - + +
148A LEU* 4.6 10.1 - - + -
151A ALA* 5.9 0.9 - - + -
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Residues in contact with ILE 129 (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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125A LEU* 2.8 48.1 + - + +
126A PHE* 3.9 3.1 - - - +
128A PHE* 1.3 77.0 - - + +
130A GLN* 1.3 64.3 + - - +
132A LYS* 3.3 8.8 + - - +
133A LYS* 3.2 18.7 + - - +
144A TRP* 3.8 15.0 - - + -
148A LEU* 4.5 13.7 - - + -
152A VAL* 3.7 22.0 - - + -
177A TRP* 3.5 46.4 - - + -
182A LEU* 3.8 18.4 - - + -
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Residues in contact with GLN 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 PHE 3.0 17.9 + - - +
127A THR* 3.9 7.4 - - - +
129A ILE* 1.3 74.3 - - - +
131A PHE* 1.3 63.4 + - + +
133A LYS* 3.2 24.2 + - - +
134A ASP* 3.0 49.9 + - - +
175A ASN* 5.1 13.5 + - + +
177A TRP* 3.3 27.1 + - + +
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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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90A GLU* 3.4 38.8 - - + -
93A LEU 3.8 5.4 - - - -
94A PHE* 3.4 45.3 - + + -
97A ALA* 3.7 14.1 - - + -
127A THR* 3.2 34.3 + - + -
128A PHE 3.1 8.4 + - - +
130A GLN* 1.3 79.6 - - + +
132A LYS* 1.3 66.3 + - - +
134A ASP* 3.2 18.0 + - + +
135A LEU* 3.0 30.1 + - - +
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Residues in contact with LYS 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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97A ALA* 4.4 6.3 - - + +
100A SER* 2.6 33.8 + - - +
101A GLN* 2.9 48.9 + - - +
112A PHE* 4.3 6.7 - - + -
128A PHE* 3.1 39.4 + - + +
129A ILE* 3.5 10.3 - - - +
130A GLN 3.3 0.2 - - - -
131A PHE* 1.3 76.0 - - - +
133A LYS* 1.3 60.6 + - - +
135A LEU* 3.4 15.1 + - - -
148A LEU* 3.7 34.3 - - + -
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Residues in contact with LYS 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 ILE 3.2 9.9 + - - +
130A GLN* 3.2 29.9 + - - +
131A PHE 3.0 0.6 - - - -
132A LYS* 1.3 74.8 - - - +
134A ASP* 1.3 67.3 + - - +
135A LEU 3.0 7.1 + - - -
177A TRP* 3.9 22.0 - - + +
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Residues in contact with ASP 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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94A PHE* 6.1 2.2 - - + -
130A GLN* 3.0 45.3 + - - +
131A PHE* 3.2 22.5 + - + +
133A LYS* 1.3 76.1 - - - +
135A LEU* 1.3 63.0 + - + +
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Residues in contact with LEU 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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94A PHE* 4.2 24.2 - - + -
97A ALA* 3.9 12.8 - - + +
98A VAL* 3.8 40.4 - - + +
101A GLN* 3.6 33.0 + - + +
131A PHE 3.0 19.1 + - - +
132A LYS 3.5 10.3 - - - +
133A LYS 3.0 6.6 - - - -
134A ASP* 1.3 84.5 - - + +
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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