Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 1IAO
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL 4.5 0.2 - - - -
13A TYR* 3.4 3.3 - - - -
14A GLN* 2.8 63.2 + - + +
16A PRO 5.5 1.8 - - - +
17A GLY* 3.8 9.2 - - - +
18A ASP* 1.3 77.3 - - - +
20A GLY* 1.3 74.1 + - - +
21A GLN* 5.3 4.5 - - + +
115A PRO* 5.4 7.0 - - + +
116A VAL* 6.0 0.9 - - + -
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Residues in contact with GLY 20 (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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12A VAL* 3.0 14.8 - - - -
13A TYR* 3.7 13.1 - - - -
18A ASP 3.8 3.2 + - - -
19A ILE* 1.3 88.6 - - - +
21A GLN* 1.3 63.5 + - - +
36A LEU* 3.6 19.0 - - - +
63A ILE* 5.0 0.2 - - - -
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Residues in contact with GLN 21 (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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10A THR 5.2 0.4 - - - +
11A THR* 3.4 3.6 - - - -
12A VAL* 2.9 49.6 + - + +
19A ILE* 5.3 4.4 - - + +
20A GLY* 1.3 74.0 - - - +
22A TYR* 1.3 66.0 + - - +
23A THR* 3.3 14.9 + - + +
33A TYR* 6.2 0.2 - - + -
36A LEU* 4.0 7.0 - - - +
63A ILE* 3.4 8.8 - - - +
115A PRO* 5.1 2.8 - - - +
136A SER* 3.1 29.3 - - - -
137A PHE* 3.3 48.0 + - - +
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Residues in contact with TYR 22 (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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9A GLY* 3.1 23.4 - - - -
10A THR 3.2 6.5 - - - -
11A THR* 3.4 19.1 - - - -
21A GLN* 1.3 76.7 - - - +
23A THR* 1.3 71.6 + - - +
24A HIS* 2.8 42.4 - + - -
32A PHE* 4.2 1.8 - + - -
33A TYR* 3.3 1.9 - - - +
34A VAL* 3.2 42.6 + - + -
36A LEU* 4.7 4.8 - - + +
54A PHE* 3.9 14.3 - + - -
58A GLY 4.5 0.2 - - - -
59A GLY* 3.4 33.7 - - - -
62A ASN* 3.7 10.5 - - + -
63A ILE* 3.9 11.0 - - + -
326B ALA* 2.9 21.1 - - - +
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Residues in contact with THR 23 (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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10A THR* 3.0 41.6 + - - +
21A GLN* 3.3 27.6 + - + +
22A TYR* 1.3 85.7 - - - +
24A HIS* 1.3 78.9 + - - +
25A GLU* 4.5 12.6 + - - +
30A GLU* 3.8 12.1 - - - +
32A PHE* 3.4 9.9 - - - -
33A TYR* 3.7 18.6 - - + +
136A SER* 3.9 2.2 - - - +
137A PHE 5.2 3.4 + - - +
138A LEU* 6.6 0.2 - - + -
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Residues in contact with HIS 24 (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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7A PHE 3.1 7.4 - - - +
8A TYR* 3.5 32.5 - + + +
9A GLY 3.1 14.1 + - - -
22A TYR* 2.8 37.2 - + - -
23A THR* 1.3 92.0 + - - +
25A GLU* 1.3 58.2 + - - +
30A GLU* 3.6 1.7 - - - +
31A LEU* 2.6 40.3 + - + +
32A PHE* 3.1 40.2 + + + +
54A PHE* 4.3 2.5 - + - -
324B SER* 3.8 14.9 + - - -
325B GLN 3.7 11.5 + - - -
326B ALA* 4.0 3.6 - - + +
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Residues in contact with GLU 25 (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 GLY* 3.7 2.3 - - - -
7A PHE* 2.9 61.0 + - + +
8A TYR* 3.8 5.2 - - - -
10A THR* 5.2 2.8 + - - +
23A THR* 4.5 14.0 + - - +
24A HIS* 1.3 78.6 - - - +
26A PHE* 1.3 62.5 + - - +
28A GLY* 3.7 24.8 - - - +
29A ASP 3.0 18.8 - - - +
30A GLU* 4.5 4.0 - - + -
31A LEU* 3.8 5.4 - - - +
137A PHE 5.4 0.3 - - - +
138A LEU* 4.4 18.0 - - + +
139A VAL* 3.7 27.4 + - - +
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Residues in contact with PHE 26 (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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4A HIS* 3.6 31.6 - + + -
5A VAL 3.8 10.8 - - - -
6A GLY* 4.0 1.3 - - - -
8A TYR* 3.3 25.6 - - - -
25A GLU* 1.3 73.9 - - - +
27A ASP* 1.3 93.7 + - + +
28A GLY 3.2 0.4 - - - -
29A ASP* 2.9 24.1 + - - +
31A LEU* 4.0 1.1 - - + +
17B TYR* 4.2 13.9 - + - -
83B TYR* 4.4 7.9 - + - -
87B GLU* 3.4 26.7 - - + +
91B SER* 3.4 33.9 - - - +
92B LEU* 4.0 16.8 - - + -
123B TYR* 4.7 3.8 - - - -
153B TRP* 3.9 8.7 - + + -
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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