Contacts of the strand formed by residues 19 - 26 (chain P) in PDB entry 2IAN
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 SER 19 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE* 4.0 14.5 - - - -
13P TYR* 3.4 5.1 - - - -
14P LEU* 2.8 44.7 + - - +
17P ASP* 4.1 18.6 - - - -
18P GLN* 1.3 78.6 - - - +
20P GLY* 1.3 59.8 + - - +
115P PRO 5.4 2.1 + - - -
116P VAL* 5.6 2.9 - - - +
137P PHE* 6.0 1.6 - - - -
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Residues in contact with GLY 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 3.5 9.6 - - - -
13P TYR* 4.0 13.4 - - - -
18P GLN 3.8 3.0 + - - -
19P SER* 1.3 78.3 + - - +
21P GLU* 1.3 65.3 + - - +
36P MET* 3.4 26.9 - - - +
63P ILE* 4.4 6.3 - - - -
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Residues in contact with GLU 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P ALA 4.3 1.1 - - - +
11P GLU* 3.1 25.3 - - - -
12P PHE* 3.1 44.9 + - + -
20P GLY* 1.3 75.7 - - - +
22P PHE* 1.3 70.1 + - - +
23P MET* 4.5 4.2 - - + +
33P HIS* 5.3 1.3 - - + -
34P VAL 5.6 1.8 - - - +
36P MET* 3.7 7.3 - - - +
63P ILE* 3.3 8.1 - - - +
136P VAL* 3.3 26.3 - - + +
137P PHE* 2.8 50.7 + - - +
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Residues in contact with PHE 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P GLN* 3.7 20.6 - - + -
10P ALA 3.8 1.8 - - - -
11P GLU* 3.1 41.7 - - + -
21P GLU* 1.3 76.9 - - - +
23P MET* 1.3 64.5 + - - +
24P PHE* 3.9 15.9 - + - -
32P PHE* 4.4 2.0 - + - -
33P HIS* 3.1 8.3 - - - +
34P VAL* 2.9 46.3 + - + -
36P MET* 3.4 19.8 - - + +
54P PHE* 3.5 23.1 - + - -
59P ALA* 3.5 28.9 - - + -
62P ASN* 4.6 2.2 - - - -
63P ILE* 4.0 6.7 - - + -
28R THR* 3.8 16.6 - - - -
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Residues in contact with MET 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P GLN* 3.4 5.4 - - - +
10P ALA* 2.8 53.1 + - + +
21P GLU* 4.5 7.0 - - + +
22P PHE* 1.3 81.9 - - - +
24P PHE* 1.3 73.3 + - - +
25P ASP* 3.8 16.6 - - + +
30P GLU* 3.7 20.4 - - + -
32P PHE* 3.4 11.9 - - - +
33P HIS* 3.9 9.2 - - + +
136P VAL* 4.4 5.2 - - + -
137P PHE 4.5 11.4 - - - +
138P LEU* 3.7 30.7 - - + -
139P PRO* 3.8 23.3 - - + -
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Residues in contact with PHE 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P ILE* 3.7 27.6 - - + -
8P ILE 3.2 4.7 - - - -
9P GLN* 3.5 20.4 - - + -
22P PHE* 3.9 14.8 - + - -
23P MET* 1.3 80.7 - - - +
25P ASP* 1.3 56.8 + - - +
30P GLU* 3.7 1.7 - - - -
31P ILE* 2.7 44.3 + - + +
32P PHE* 3.0 51.8 + + + +
54P PHE* 4.4 3.6 - + - -
78Q TYR* 3.4 23.8 - + - -
82Q ASN* 3.9 16.2 - - + -
26R ILE* 4.3 5.6 - - + -
27R GLY 3.3 24.2 - - - -
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Residues in contact with ASP 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P VAL 3.4 2.4 - - - +
7P ILE* 3.3 4.8 - - - -
8P ILE* 2.7 53.5 + - + +
23P MET* 3.8 16.4 - - - +
24P PHE* 1.3 71.8 - - - +
26P PHE* 1.3 57.4 + - - +
27P ASP 4.1 0.2 + - - -
28P GLY* 2.6 42.8 + - - -
29P ASP 3.5 5.0 - - - -
30P GLU 5.1 0.2 + - - -
31P ILE* 4.9 0.4 - - - -
138P LEU* 4.3 1.6 - - - +
139P PRO* 3.2 33.5 - - + +
146P ARG* 3.8 12.5 + - - -
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Residues in contact with PHE 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P HIS* 3.6 26.7 - + + -
6P VAL 3.3 7.2 - - - -
7P ILE* 3.7 27.1 - - + +
24P PHE 4.0 1.8 + - - -
25P ASP* 1.3 71.4 - - - +
27P ASP* 1.3 86.2 + - - +
28P GLY 3.0 0.2 - - - -
29P ASP* 2.8 27.1 + - - +
31P ILE* 3.9 16.5 - - + +
83Q TYR* 6.0 0.7 - + - -
90Q THR* 3.6 41.7 - - + -
91Q VAL* 3.8 13.9 - - + -
123Q TYR* 3.1 26.2 - - - -
153Q TRP* 3.5 21.1 - + + -
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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