Contacts of the strand formed by residues 6 - 14 (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 GLY 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL* 1.3 75.5 - - - +
7A PHE* 1.3 67.9 - - - -
8A TYR* 3.6 33.3 + - - -
25A GLU 3.7 3.8 - - - -
26A PHE* 4.0 2.7 - - - -
14B GLU* 3.6 0.3 - - - -
15B CYS 2.7 35.8 + - - -
17B TYR* 3.6 4.0 - - - -
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Residues in contact with PHE 7 (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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5A VAL* 3.7 24.7 - - + -
6A GLY* 1.3 79.8 - - - -
8A TYR* 1.3 60.9 + - - +
10A THR* 3.9 14.1 + - - +
24A HIS* 3.1 9.2 - - - -
25A GLU* 2.9 69.7 + - + +
28A GLY* 5.5 8.1 - - - -
139A VAL* 3.7 26.2 - - + -
141A ARG* 6.3 2.9 - - + -
13B GLY 3.5 4.0 - - - -
14B GLU* 3.3 38.8 - - + -
16B TYR* 4.7 4.0 - + - -
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Residues in contact with TYR 8 (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* 3.6 17.6 + - - -
7A PHE* 1.3 73.9 - - - +
9A GLY* 1.3 57.7 + - - +
10A THR 3.7 0.4 - - - -
24A HIS* 3.5 32.3 - + - +
25A GLU 3.8 13.9 - - - -
26A PHE* 3.3 12.1 - - - -
31A LEU* 4.0 6.3 - - + -
13B GLY* 3.2 13.1 + - - -
15B CYS* 4.7 7.9 - - + -
17B TYR* 3.1 26.5 + - - -
78B ALA* 4.6 5.4 - - + -
79B CYS* 5.1 2.5 - - - -
82B ASN* 3.3 33.6 - - + +
87B GLU* 3.0 39.4 - - + +
325B GLN 3.9 4.5 - - - +
327B VAL* 3.1 36.0 + - + +
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Residues in contact with GLY 9 (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 TYR* 1.3 74.4 - - - +
10A THR* 1.3 56.9 + - - +
11A THR* 2.8 26.2 + - - -
22A TYR* 3.1 23.1 - - - -
23A THR 3.9 0.2 + - - -
24A HIS* 3.1 10.3 + - - -
62A ASN* 3.2 16.4 + - - -
11B PHE* 3.3 12.5 - - - -
13B GLY 4.6 1.1 - - - -
327B VAL 4.0 6.3 - - - -
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Residues in contact with THR 10 (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* 3.9 25.6 + - - +
8A TYR 3.7 0.4 - - - -
9A GLY* 1.3 70.8 - - - +
11A THR* 1.3 63.5 + - - +
12A VAL* 5.4 6.5 - - + -
21A GLN* 4.4 0.9 - - - +
22A TYR* 3.2 6.6 - - - -
23A THR* 3.0 48.0 + - - +
25A GLU* 5.2 2.7 + - - +
139A VAL* 4.4 30.5 - - + -
145A PHE* 6.2 0.2 - - + -
10B GLN* 6.3 1.1 - - + -
11B PHE 3.4 12.6 - - - +
12B LYS* 4.7 10.0 - - + +
13B GLY 4.5 5.5 + - - +
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Residues in contact with THR 11 (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 2.8 15.9 + - - -
10A THR* 1.3 75.2 - - - +
12A VAL* 1.3 69.9 + - - +
13A TYR* 5.5 0.2 - - + -
21A GLN 3.4 3.4 - - - -
22A TYR* 3.4 4.5 - - - -
62A ASN* 3.2 18.8 + - - +
63A ILE* 3.4 37.5 - - + -
66A GLU* 3.6 30.4 - - + +
10B GLN* 3.1 6.9 - - - +
11B PHE* 2.9 34.3 + - - +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 5.4 7.4 - - + -
11A THR* 1.3 84.4 - - - +
13A TYR* 1.3 71.2 + - - +
14A GLN* 4.9 2.7 - - + +
20A GLY* 3.0 24.0 - - - -
21A GLN* 2.9 36.5 + - + +
66A GLU* 5.6 0.2 - - - -
115A PRO* 4.0 25.4 - - + -
137A PHE 5.8 0.2 - - - +
145A PHE* 3.9 28.7 - - + -
8B VAL* 4.0 11.2 - - + -
9B VAL 3.5 11.2 - - - +
10B GLN* 4.2 3.1 - - + -
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Residues in contact with TYR 13 (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* 1.3 80.7 - - - +
14A GLN* 1.3 67.1 + - - +
15A SER* 5.5 1.1 - - - -
18A ASP* 3.3 40.3 + - + +
19A ILE 3.4 3.1 - - - -
20A GLY* 3.7 16.4 - - - -
36A LEU* 6.0 0.4 - - + -
63A ILE* 3.6 32.8 - - + -
66A GLU* 4.3 8.5 - - + -
67A LYS* 2.6 55.4 + - + +
70A LEU* 4.0 16.6 - - + +
7B PHE 3.7 0.3 - - - +
8B VAL* 3.2 4.2 - - - +
9B VAL* 2.9 49.6 + - + +
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Residues in contact with GLN 14 (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* 4.9 2.9 - - + +
13A TYR* 1.3 82.1 - - - +
15A SER* 1.3 61.9 + - - +
16A PRO* 4.4 5.5 - - + +
17A GLY 4.2 0.3 + - - -
18A ASP* 3.2 24.1 + - - -
19A ILE* 2.8 40.5 + - + +
70A LEU* 4.2 2.7 - - - -
114A PRO* 3.4 24.0 - - - +
115A PRO* 3.5 37.6 - - + +
116A VAL* 3.7 13.0 - - - +
168A TRP* 6.3 0.2 - - - -
6B HIS* 5.8 3.6 - - - +
7B PHE 3.0 7.8 + - - +
8B VAL* 3.6 19.9 - - + +
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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