Contacts of the helix formed by residues 86 - 104 (chain A) in PDB entry 1IOU
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LYS 5.0 0.2 - - - -
84A GLN 3.7 7.6 - - - +
85A TYR* 1.3 106.2 - - - +
87A VAL* 1.3 62.0 + - + +
88A ARG* 4.4 8.3 - - + +
89A PRO* 3.2 27.9 - - + +
90A ALA 3.8 2.1 + - - -
135A PRO* 3.1 25.6 - - + +
136A SER* 4.2 5.4 - - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 5.3 1.3 - - - +
67A HIS* 3.7 24.9 - - + +
69A TYR* 3.2 24.0 - - + +
85A TYR 4.3 0.9 - - - +
86A PRO* 1.3 72.9 - - + +
88A ARG* 1.3 56.6 + - + +
89A PRO 3.4 0.2 - - - -
90A ALA* 3.0 6.3 + - - +
91A TYR* 2.7 39.1 + - + +
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 4.7 6.3 - - + -
87A VAL* 1.3 80.6 - - + +
89A PRO* 1.3 64.8 - - + +
91A TYR* 2.9 27.7 + - - +
92A THR* 3.1 7.2 + - - +
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Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 5.1 1.8 - - + -
86A PRO* 3.2 21.8 - - + +
88A ARG* 1.3 91.8 - - + +
90A ALA* 1.3 53.1 + - - +
91A TYR 3.0 2.0 - - - -
92A THR* 2.7 30.0 - - + +
93A LEU* 2.7 20.8 + - - +
132A TYR* 3.3 21.2 + - + -
135A PRO 3.7 5.4 - - - +
136A SER* 2.8 43.7 - - - +
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Residues in contact with ALA 90 (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 HIS* 4.2 10.3 - - + -
69A TYR* 2.7 43.9 - - + +
79A LEU* 4.7 4.9 - - + -
85A TYR* 3.9 18.3 - - + -
86A PRO 3.8 12.2 + - - +
87A VAL* 3.0 8.0 + - - +
89A PRO* 1.3 80.5 - - - +
91A TYR* 1.3 56.0 + - - +
93A LEU* 3.4 9.2 + - - +
94A LEU 2.9 16.8 + - - -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 4.3 23.8 + - - -
69A TYR* 4.1 6.7 - + - +
87A VAL* 2.7 15.1 + - + +
88A ARG* 2.9 18.2 - - - +
90A ALA* 1.3 76.3 - - - +
92A THR* 1.3 58.1 + - - +
94A LEU* 2.9 35.3 + - + +
95A ASN* 2.9 41.6 + - - +
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Residues in contact with THR 92 (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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88A ARG 3.1 3.2 + - - +
89A PRO* 2.7 38.1 - - + +
91A TYR* 1.3 79.0 - - - +
93A LEU* 1.3 56.4 + - - +
95A ASN* 2.8 34.7 + - - +
96A LYS* 3.0 17.2 + - - +
132A TYR* 3.2 13.2 - - + +
139A ASP* 3.6 18.6 + - - +
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Residues in contact with LEU 93 (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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6A ILE* 3.1 29.8 - - + -
79A LEU* 3.5 20.2 - - + -
85A TYR* 3.9 6.7 - - - +
89A PRO 2.7 17.4 + - - +
90A ALA 3.5 7.0 - - - +
92A THR* 1.3 76.8 - - - +
94A LEU* 1.3 59.0 + - - +
96A LYS* 4.2 0.5 - - - +
97A ILE* 2.9 45.0 + - + +
128A TYR* 4.0 17.4 - - + -
132A TYR* 3.0 47.8 - - + -
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Residues in contact with LEU 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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56A ARG* 4.8 2.9 - - - +
69A TYR* 3.0 60.6 - - + -
70A ALA 4.7 3.4 - - - +
79A LEU* 4.9 0.2 - - - -
90A ALA 2.9 5.4 + - - +
91A TYR* 2.9 44.6 + - + +
93A LEU* 1.3 78.6 - - - +
95A ASN* 1.3 62.0 + - - +
97A ILE* 3.2 19.9 - - - +
98A LEU* 3.2 34.9 + - + +
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Residues in contact with ASN 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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91A TYR* 2.9 34.5 + - - -
92A THR* 2.8 20.1 + - - +
94A LEU* 1.3 80.5 - - - +
96A LYS* 1.3 66.1 + - + +
98A LEU* 4.2 1.1 - - - +
99A ASP* 3.0 27.8 + - - +
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Residues in contact with LYS 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 THR* 3.0 13.1 + - - +
95A ASN* 1.3 80.0 - - + +
97A ILE* 1.3 51.3 + - - +
99A ASP* 3.8 4.4 - - - +
100A GLU* 2.6 40.8 + - - +
124A GLN* 4.0 5.8 - - - +
128A TYR* 3.1 43.7 - - + +
139A ASP* 4.2 22.2 + - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.4 2.9 - - + -
7A GLY 3.9 9.9 - - - +
8A VAL* 4.5 3.6 - - + -
69A TYR* 5.9 0.7 - - + -
77A GLY* 5.9 1.8 - - - -
78A VAL 5.8 0.7 - - - +
79A LEU* 5.0 4.9 - - + -
93A LEU* 2.9 42.1 + - + +
94A LEU* 3.2 18.4 - - - +
96A LYS* 1.3 73.9 - - - +
98A LEU* 1.3 79.0 + - + +
99A ASP 3.1 1.1 - - - -
100A GLU* 2.8 1.4 + - - -
101A TYR* 2.7 33.7 + - - +
122A MET* 2.8 32.2 - - + +
124A GLN* 5.4 0.9 - - - +
125A LEU* 3.0 41.1 - - + +
128A TYR* 5.0 2.2 - - + -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.3 11.2 - - + -
69A TYR* 3.8 4.5 - - + +
70A ALA 3.6 23.8 - - - +
71A ARG* 3.7 20.9 - - + -
75A ILE* 4.4 9.4 - - + +
76A CYS 4.4 2.2 - - - -
77A GLY* 4.2 26.7 - - - +
94A LEU* 3.2 36.7 + - + +
95A ASN* 4.3 1.3 - - - +
97A ILE* 1.3 90.6 - - + +
99A ASP* 1.3 51.3 + - - +
101A TYR* 4.0 4.1 - - + +
102A LEU* 2.8 43.3 + - + +
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Residues in contact with ASP 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 ASN* 3.0 20.8 + - - +
96A LYS* 3.8 5.6 - - - +
98A LEU* 1.3 76.7 - - - +
100A GLU* 1.3 55.8 + - - +
102A LEU* 3.3 16.4 - - - +
103A VAL* 2.7 56.3 + - - +
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Residues in contact with GLU 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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96A LYS 2.6 24.6 + - - +
97A ILE 2.8 4.5 + - - +
99A ASP* 1.3 73.1 - - - +
101A TYR* 1.3 58.9 + - - +
103A VAL* 4.2 9.7 - - - +
104A ALA* 3.0 33.6 + - + +
122A MET* 3.3 25.7 - - + +
123A LYS 5.0 0.7 + - - -
124A GLN* 3.1 48.1 + - + +
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Residues in contact with TYR 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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8A VAL* 4.0 8.5 - - + -
19A LEU* 2.8 49.7 - - + +
20A SER* 3.9 9.6 - - - -
75A ILE* 3.3 32.3 - - + -
97A ILE 2.7 18.3 + - - +
98A LEU* 4.0 7.2 - - - +
100A GLU* 1.3 75.3 - - - +
102A LEU* 1.3 53.0 + - - +
104A ALA* 3.9 1.6 - - - +
105A HIS* 2.7 60.2 + + - -
110A TRP* 4.1 5.8 - + + -
113A VAL* 3.0 19.4 - - + +
116A THR* 3.4 14.5 + - + +
121A LYS* 4.8 4.7 - - + -
122A MET* 3.4 29.6 - - + +
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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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71A ARG* 6.4 1.6 - - + -
73A GLU* 4.0 19.3 - - - +
75A ILE* 5.5 1.8 - - + -
98A LEU* 2.8 32.9 + - + +
99A ASP* 3.3 27.4 - - + +
101A TYR* 1.3 78.6 - - + +
103A VAL* 1.3 67.8 + - + +
105A HIS 2.4 26.4 - - - +
106A PRO* 3.9 4.0 - - - +
107A LYS* 4.2 18.3 + - + +
110A TRP* 3.1 34.9 + - + +
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Residues in contact with VAL 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 ASP* 2.7 43.0 + - - +
100A GLU* 3.9 12.1 - - - +
101A TYR 3.3 0.2 - - - -
102A LEU* 1.3 81.4 - - + +
104A ALA* 1.3 57.8 + - - +
105A HIS* 2.6 21.2 + - - -
106A PRO* 4.4 2.1 - - - +
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Residues in contact with ALA 104 (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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100A GLU* 3.0 22.3 + - + +
101A TYR* 3.9 2.9 - - - +
102A LEU 3.5 0.2 - - - -
103A VAL* 1.3 77.8 - - - +
105A HIS* 1.3 72.4 + - + +
121A LYS* 4.4 22.7 + - - +
122A MET* 5.8 3.4 - - + +
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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