Contacts of the helix formed by residues 93 - 103 (chain A) in PDB entry 1IXR
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 PRO 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LEU 5.3 0.9 - - - +
91A ALA 4.0 4.9 - - - +
92A LEU* 1.3 87.5 - - + +
94A PRO* 1.3 72.7 - - + +
95A ARG* 3.0 37.9 + - + +
96A LEU* 3.1 27.1 + - + -
97A LEU* 2.9 18.2 + - - +
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Residues in contact with PRO 94 (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 ASP* 6.0 0.2 - - - +
66A GLU* 4.0 20.2 - - + +
67A ASN* 3.6 22.9 - - - +
70A LEU* 3.3 30.0 - - + +
89A LEU* 5.3 3.3 - - + +
92A LEU 3.7 1.5 - - - +
93A PRO* 1.3 81.1 - - + +
95A ARG* 1.3 90.5 - - - +
97A LEU* 3.5 5.2 - - + +
98A ALA* 2.8 38.8 + - - +
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Residues in contact with ARG 95 (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 ASP* 5.9 0.8 + - - -
66A GLU* 5.8 0.6 - - - +
93A PRO* 3.0 21.5 - - + +
94A PRO* 1.3 101.7 - - - +
96A LEU* 1.3 81.8 + - + +
98A ALA* 3.8 3.7 - - - +
99A ARG* 2.9 26.8 + - - +
135A LEU* 5.0 17.4 - - - +
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Residues in contact with LEU 96 (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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92A LEU* 4.5 14.8 - - + -
93A PRO* 3.1 32.2 + - + +
95A ARG* 1.3 95.9 - - + +
97A LEU* 1.3 52.5 + - - +
99A ARG* 3.3 6.4 + - - +
100A ALA* 2.6 40.1 + - - +
108A LEU* 4.8 15.2 - - + +
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Residues in contact with LEU 97 (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 LEU* 4.1 13.2 - - + -
74A LEU* 4.2 17.0 - - + -
88A LEU* 4.5 9.2 - - + +
89A LEU* 4.4 26.7 - - + +
92A LEU* 4.3 20.7 - - + +
93A PRO 2.9 12.9 + - - +
94A PRO* 3.5 8.7 - - + +
96A LEU* 1.3 74.9 - - - +
98A ALA* 1.3 52.9 + - - +
100A ALA* 2.5 11.1 + - - -
101A LEU* 2.4 73.2 + - + -
109A LEU* 3.8 22.9 - - + -
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Residues in contact with ALA 98 (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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66A GLU* 5.4 4.0 - - - +
70A LEU* 3.9 11.8 - - + +
94A PRO 2.8 21.3 + - - +
95A ARG* 3.9 2.7 - - - +
97A LEU* 1.3 72.5 - - - +
99A ARG* 1.3 57.9 + - - +
101A LEU* 3.4 12.7 - - - +
102A LEU* 2.9 34.5 + - - +
131A VAL* 3.2 12.6 - - + +
132A PRO 5.8 0.9 - - - +
134A HIS 5.6 0.7 - - - +
135A LEU* 3.9 24.7 - - + -
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Residues in contact with ARG 99 (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 2.9 21.5 + - - +
96A LEU* 3.7 5.6 - - - +
98A ALA* 1.3 73.7 - - - +
100A ALA* 1.3 58.8 + - - +
102A LEU* 4.6 1.1 - - - -
103A GLU* 2.8 53.4 + - + +
135A LEU* 3.9 20.5 - - + +
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Residues in contact with ALA 100 (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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92A LEU* 5.2 0.7 - - + -
96A LEU 2.6 19.3 + - - +
97A LEU* 2.5 18.8 + - - +
99A ARG* 1.3 68.5 - - - +
101A LEU* 1.3 71.9 + - - +
103A GLU* 4.9 0.2 - - - -
104A GLY 2.5 15.9 + - - -
105A ASP* 2.6 38.2 + - + +
108A LEU* 4.4 13.9 - - + -
109A LEU* 4.7 11.0 - - + -
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Residues in contact with LEU 101 (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 LEU* 3.5 22.2 - - + +
73A LEU* 5.2 5.4 - - + -
74A LEU* 4.2 20.9 - - + -
88A LEU* 5.7 0.2 - - + -
97A LEU* 2.4 58.6 + - + +
98A ALA* 3.4 8.1 - - - +
100A ALA* 1.3 68.0 - - - +
102A LEU* 1.3 55.1 + - - +
104A GLY* 2.4 32.4 + - - -
105A ASP 4.9 0.2 - - - +
109A LEU* 4.7 11.0 - - + -
123A ILE* 4.7 6.7 - - + -
124A ALA* 4.6 10.9 - - - +
127A LEU* 3.9 25.0 - - + +
128A LYS* 6.0 0.3 - - - -
131A VAL* 3.5 18.4 - - + -
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Residues in contact with LEU 102 (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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98A ALA 2.9 13.5 + - - +
99A ARG 4.0 0.7 - - - +
101A LEU* 1.3 75.0 - - - +
103A GLU* 1.3 89.1 + - + +
104A GLY* 2.7 10.0 + - - -
127A LEU 5.4 1.6 - - - -
128A LYS* 5.2 3.3 - - - -
129A GLY* 4.8 13.7 + - - +
131A VAL* 3.0 40.2 - - + +
133A PRO* 5.0 8.3 - - + -
135A LEU* 3.6 27.8 - - + -
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Residues in contact with GLU 103 (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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99A ARG* 2.8 44.9 + - + +
100A ALA* 3.3 2.5 - - - +
102A LEU* 1.3 91.4 - - + +
104A GLY* 1.3 66.0 + - - +
105A ASP* 3.4 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