Contacts of the helix formed by residues 113 - 124 (chain A) in PDB entry 3IH9
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LYS* 3.7 1.6 - - - -
92A SER* 4.0 26.7 - - - +
93A GLY 4.2 7.6 - - - +
94A GLU* 3.5 14.1 - - - +
96A PHE* 6.0 2.9 - - + -
108A PRO* 4.7 0.9 - - + -
109A ASP* 4.3 21.5 - - + +
110A ASN* 3.3 28.3 - - - +
112A MET* 1.3 79.8 - - - +
114A ASN* 1.3 66.5 + - - +
115A ALA* 4.4 11.2 - - + -
116A GLY* 2.8 20.9 + - - +
117A ALA* 2.9 10.6 + - - +
240A SER* 5.8 0.4 - - - +
243A TYR* 3.8 28.5 - - + -
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Residues in contact with ASN 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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64A SER* 4.3 2.1 + - - -
67A LYS* 2.7 33.7 + - - +
94A GLU* 2.9 29.0 + - - +
113A ILE* 1.3 70.2 - - - +
115A ALA* 1.3 64.7 + - - +
117A ALA* 2.8 14.1 + - - +
118A LEU* 2.8 17.5 + - + +
166A ARG* 3.4 16.8 - - - +
167A ASN* 3.2 24.6 + - - +
170A LEU* 3.5 13.2 - - + -
191A TYR* 3.3 14.0 + - + -
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Residues in contact with ALA 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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94A GLU* 4.5 2.0 + - - +
96A PHE* 4.4 16.6 - - + -
108A PRO* 3.8 17.1 - - + +
113A ILE* 3.3 10.3 - - + +
114A ASN* 1.3 77.0 - - - +
116A GLY* 1.3 62.2 + - - +
118A LEU* 4.3 1.8 - - - -
119A ALA* 3.3 18.7 + - - +
170A LEU* 3.8 24.9 - - + +
174A LEU* 3.4 28.0 - - + +
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Residues in contact with GLY 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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87A VAL* 4.2 3.3 - - - +
108A PRO* 3.8 15.6 - - - +
110A ASN 3.1 26.5 - - - -
111A ALA* 4.2 4.0 - - - -
113A ILE* 2.8 9.6 + - - +
115A ALA* 1.3 81.8 - - - +
117A ALA* 1.3 55.6 + - - +
119A ALA* 3.4 3.6 + - - +
120A VAL* 3.1 30.5 + - - +
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Residues in contact with ALA 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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67A LYS* 3.6 30.3 - - + -
70A THR* 5.6 1.0 + - - +
111A ALA 4.1 4.4 + - - +
113A ILE 2.9 3.8 + - - +
114A ASN 2.8 8.1 + - - +
116A GLY* 1.3 74.4 - - - +
118A LEU* 1.3 61.9 + - - +
120A VAL* 3.1 8.2 + - - +
121A HIS* 2.9 30.5 + - - +
191A TYR* 3.4 30.4 - - + -
194A GLN* 5.1 3.2 + - - +
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Residues in contact with LEU 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 ASN 2.8 21.9 + - - +
115A ALA* 3.7 5.4 - - - +
117A ALA* 1.3 77.5 - - - +
119A ALA* 1.3 62.6 + - - +
121A HIS* 3.6 1.7 + - - -
122A GLN* 3.2 18.5 + - - +
167A ASN* 3.8 18.8 - - + +
170A LEU* 3.7 33.0 - - + -
171A ALA* 4.0 6.5 - - + +
174A LEU* 4.0 8.3 - - + -
180A LEU* 3.6 4.8 - - + +
187A ILE* 3.4 32.8 - - + +
188A VAL* 4.1 13.7 - - + -
191A TYR* 3.7 35.0 - - + -
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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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86A GLN* 4.2 3.8 - - + +
87A VAL* 4.1 15.3 - - + -
108A PRO* 4.1 5.4 - - + -
115A ALA 3.3 10.2 + - - +
116A GLY 3.6 9.0 - - - +
117A ALA 3.2 0.2 - - - -
118A LEU* 1.3 78.0 - - - +
120A VAL* 1.3 62.6 + - - +
122A GLN* 3.5 4.7 + - - +
123A LEU* 3.3 27.7 + - - +
174A LEU* 4.5 0.9 - - + +
179A VAL* 3.7 28.2 - - + +
180A LEU* 4.1 10.7 - - - +
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Residues in contact with VAL 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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67A LYS 5.1 1.1 - - - +
70A THR* 3.5 44.4 - - - +
71A TYR* 3.6 25.1 - - + +
74A ALA* 4.0 6.0 - - + +
83A VAL* 5.2 0.7 - - + -
87A VAL* 3.9 16.8 - - + -
111A ALA* 4.1 10.3 - - + +
116A GLY 3.1 15.7 + - - +
117A ALA* 3.1 10.5 + - - +
119A ALA* 1.3 73.9 - - - +
121A HIS* 1.3 67.0 + - - +
123A LEU* 2.9 22.0 + - + +
124A LEU* 3.2 10.7 + - + +
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Residues in contact with HIS 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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117A ALA 2.9 15.8 + - - +
118A LEU* 3.9 7.0 - - - +
120A VAL* 1.3 77.0 - - - +
122A GLN* 1.3 59.3 + - - +
124A LEU* 2.9 46.7 + - + +
131A ARG 5.2 1.6 - - - -
134A ARG* 3.7 39.0 + - + +
135A LEU* 4.3 8.0 - - - -
138A ALA* 4.6 0.6 - - + +
186A GLU 5.6 0.4 - - - -
187A ILE* 4.5 13.6 + - + +
190A GLY* 3.1 41.0 + - - -
191A TYR* 3.8 9.2 + - + -
194A GLN* 2.8 31.0 - - + +
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Residues in contact with GLN 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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78A ARG* 5.3 1.2 + - - -
118A LEU 3.2 3.5 + - - +
119A ALA 3.5 8.5 - - - +
120A VAL 3.2 0.8 - - - -
121A HIS* 1.3 78.9 + - - +
123A LEU* 1.3 59.8 + - + +
126A GLY 4.7 0.5 - - - +
127A PRO* 5.7 1.4 + - - +
134A ARG* 3.0 26.5 + - - +
179A VAL 4.3 2.9 - - - +
180A LEU* 3.4 29.2 - - + -
181A GLN* 3.2 36.0 + - - +
182A ASP* 3.0 45.0 + - - +
187A ILE* 3.6 25.3 - - + +
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Residues in contact with LEU 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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74A ALA* 4.4 6.5 - - + +
78A ARG* 2.9 57.6 + - + +
82A ALA* 3.9 21.8 - - + +
83A VAL* 4.1 30.1 - - + -
86A GLN* 3.9 24.2 - - + -
87A VAL* 4.3 1.8 - - + -
119A ALA 3.3 19.1 - - - +
120A VAL* 2.9 16.1 + - - +
122A GLN* 1.3 81.6 - - + +
124A LEU* 1.3 62.4 + - - +
125A VAL 3.4 1.8 - - - -
134A ARG* 4.2 0.7 - - - -
181A GLN* 5.9 3.1 - - - +
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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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70A THR* 3.6 32.5 - - + +
73A ALA* 3.9 17.3 - - + -
74A ALA* 4.0 7.2 - - + +
77A ASP* 2.4 31.0 - - - +
120A VAL 3.2 4.1 + - - +
121A HIS* 2.9 48.3 + - + +
122A GLN 3.3 1.2 + - - -
123A LEU* 1.3 76.5 - - - +
125A VAL* 1.3 58.2 + - - +
134A ARG* 3.4 34.5 - - + +
137A ARG* 3.6 8.3 - - + +
138A ALA* 3.9 14.8 - - + +
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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