Contacts of the strand formed by residues 5 - 15 (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 HIS 5 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3P GLU* 3.5 8.3 - - - +
4P GLU* 1.3 113.1 + - + +
6P VAL* 1.3 63.8 + - - +
26P PHE* 3.6 21.4 - + + -
27P ASP* 2.7 28.5 + - - +
16Q HIS* 3.6 0.5 - - - -
17Q PHE* 3.1 49.1 + - + -
20Q GLY 5.8 1.6 - - - -
83Q TYR* 4.4 11.7 - + + -
90Q THR 5.7 0.2 - - - -
91Q VAL* 3.7 35.5 + - + +
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Residues in contact with VAL 6 (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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3P GLU* 3.3 25.6 - - - +
5P HIS* 1.3 74.9 - - - +
7P ILE* 1.3 65.2 + - - +
8P ILE* 3.5 31.8 - - + +
25P ASP* 3.4 1.8 - - - +
26P PHE* 3.3 5.6 - - - -
27P ASP* 2.9 39.6 + - - +
14Q GLU* 4.6 0.7 - - + -
15Q CYS 3.3 9.2 - - - +
16Q HIS* 3.9 25.8 - - + +
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Residues in contact with ILE 7 (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* 1.3 72.5 - - - +
8P ILE* 1.3 62.7 + - - +
24P PHE* 3.7 30.1 - - + -
25P ASP 3.3 6.1 - - - +
26P PHE* 3.7 29.8 - - + -
31P ILE* 5.2 9.2 - - + -
13Q PHE 3.5 1.6 - - - +
15Q CYS* 2.7 43.7 + - + +
17Q PHE* 3.8 24.4 - - + -
82Q ASN* 4.2 17.3 - - + +
83Q TYR* 4.2 25.1 - - + +
86Q GLY* 6.0 2.2 - - - -
90Q THR* 5.7 1.6 - - - +
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Residues in contact with ILE 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P VAL* 3.5 23.8 - - + +
7P ILE* 1.3 78.7 - - - +
9P GLN* 1.3 62.2 + - - +
10P ALA* 3.7 5.5 + - + -
23P MET* 3.6 1.4 - - - +
24P PHE* 3.2 7.5 - - - -
25P ASP* 2.7 58.4 + - + +
139P PRO* 4.9 14.6 - - + -
141P GLU* 5.4 3.4 - - - +
12Q LYS* 3.8 22.4 - - + +
13Q PHE 3.1 14.8 - - - +
14Q GLU* 3.6 31.9 - - + +
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Residues in contact with GLN 9 (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 4.2 0.4 - - - -
8P ILE* 1.3 71.7 - - - +
10P ALA* 1.3 58.5 + - - +
11P GLU* 2.5 29.4 + - - +
22P PHE* 3.7 20.3 - - + -
23P MET 3.4 4.9 - - - +
24P PHE* 3.5 24.7 - - + -
62P ASN* 3.7 0.2 - - - +
11Q LEU 3.8 1.4 - - - +
12Q LYS* 3.1 3.8 - - - -
13Q PHE* 2.6 61.4 + - + -
78Q TYR* 2.4 39.2 + - - +
28R THR* 3.7 3.4 - - - +
29R LEU 3.0 30.2 + - - +
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Residues in contact with ALA 10 (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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8P ILE* 3.7 3.6 + - + +
9P GLN* 1.3 75.0 - - - +
11P GLU* 1.3 62.9 + - - +
12P PHE* 5.7 1.4 - - - -
21P GLU* 3.8 2.1 - - - +
22P PHE* 3.8 1.6 - - - -
23P MET* 2.8 55.1 + - + +
139P PRO* 4.1 21.5 - - + -
11Q LEU 3.7 3.1 - - - -
12Q LYS* 4.2 15.3 - - + +
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Residues in contact with GLU 11 (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* 2.5 31.9 + - - +
10P ALA* 1.3 77.8 - - - +
12P PHE* 1.3 61.6 + - - +
21P GLU 3.1 8.7 - - - +
22P PHE* 3.1 29.5 - - + -
62P ASN* 2.7 30.4 + - - +
63P ILE* 4.1 0.9 - - + -
66P ASP* 2.6 40.4 - - - +
10Q GLN* 3.4 6.6 - - - +
11Q LEU* 2.9 44.1 + - + +
12Q LYS* 5.3 0.3 - - - +
13Q PHE* 4.2 0.3 - - - -
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Residues in contact with PHE 12 (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 5.7 1.3 - - - -
11P GLU* 1.3 75.7 - - - +
13P TYR* 1.3 74.5 + - - +
14P LEU* 4.3 5.2 - - + -
19P SER* 4.0 27.6 - - - -
20P GLY* 3.5 2.9 - - - -
21P GLU* 3.1 76.5 + - + +
63P ILE* 4.5 4.5 - - - +
66P ASP* 4.8 4.4 - - - +
115P PRO* 3.6 38.6 - - + -
137P PHE* 4.2 10.3 - + + -
145P PHE* 4.0 14.6 - + + -
8Q LEU* 4.1 6.7 - - + -
9Q TRP 3.1 11.7 - - - +
10Q GLN* 3.6 15.5 - - + -
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Residues in contact with TYR 13 (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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12P PHE* 1.3 74.8 - - - +
14P LEU* 1.3 69.4 + - - +
15P ASN* 3.6 17.0 - - - -
18P GLN* 3.5 39.6 + - + +
19P SER 3.4 9.9 - - - -
20P GLY* 4.0 6.1 - - - -
63P ILE* 3.8 30.5 - - + -
66P ASP* 4.1 8.3 - - + +
67P LYS* 3.6 59.0 + - + +
70P LEU* 3.4 22.2 - - + +
8Q LEU* 3.7 1.6 - - - +
9Q TRP* 2.9 34.0 + - + +
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Residues in contact with LEU 14 (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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12P PHE* 4.3 6.3 - - + -
13P TYR* 1.3 79.4 - - - +
15P ASN* 1.3 59.4 + - - +
17P ASP* 3.4 24.7 - - + +
18P GLN* 2.9 24.1 + - - -
19P SER* 2.8 24.4 + - - +
114P PRO* 4.6 4.7 - - + -
115P PRO* 4.1 23.3 - - + +
116P VAL* 3.4 29.6 - - + -
6Q ARG* 3.9 27.1 - - + -
7Q PHE 3.7 2.7 - - - +
8Q LEU* 4.0 26.2 - - + -
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Residues in contact with ASN 15 (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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13P TYR* 3.6 18.5 - - - -
14P LEU* 1.3 74.6 - - - +
16P PRO* 1.3 73.8 - - + +
17P ASP* 2.8 25.6 - - - +
18P GLN* 4.1 13.3 + - - +
67P LYS* 4.7 4.5 + - - -
70P LEU* 3.7 16.7 - - + +
71P GLU* 3.8 29.7 + - - +
74P THR* 5.3 3.6 + - - +
6Q ARG* 3.7 5.9 - - - +
7Q PHE* 3.0 25.9 + - + +
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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