Contacts of the strand formed by residues 19 - 26 (chain C) in PDB entry 1I3R
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 ARG 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.8 9.3 - - + -
13C TYR* 3.3 4.6 - - - -
14C LEU* 2.6 43.9 + - + +
17C ASP* 3.6 32.1 + - + +
18C LYS* 1.3 81.2 - - - +
20C GLY* 1.3 58.0 + - - +
21C GLU* 6.1 0.9 - - + -
36C ILE* 4.3 5.8 - - - -
115C PRO 5.6 1.8 + - - +
116C VAL* 3.9 23.9 - - + +
137C PHE* 5.7 6.3 - - - -
1J NAG 6.1 1.2 - - - -
2J NAG 4.2 22.8 - - - +
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Residues in contact with GLY 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.2 15.7 - - - -
13C TYR* 4.1 8.5 - - - -
19C ARG* 1.3 76.7 - - - +
21C GLU* 1.3 72.4 + - - +
36C ILE* 2.9 39.8 - - - +
63C ILE* 4.5 3.6 - - - -
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA 4.4 0.7 - - - -
11C GLN* 3.1 6.0 - - - -
12C PHE* 3.1 53.6 + - + -
19C ARG* 6.1 0.7 - - + -
20C GLY* 1.3 85.5 - - - +
22C PHE* 1.3 63.4 + - - +
23C MET* 5.9 3.0 - - + +
33C HIS* 6.3 1.8 - - + -
34C VAL 4.8 3.4 - - - +
36C ILE* 4.2 4.0 - - - -
63C ILE* 3.2 9.0 - - - +
136C VAL* 3.5 24.7 - - + +
137C PHE* 3.1 51.5 + - - +
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Residues in contact with PHE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLN* 3.5 41.7 - - + -
10C ALA 3.5 3.6 - - - -
11C GLN* 3.6 18.8 - - + -
21C GLU* 1.3 76.7 - - - +
23C MET* 1.3 65.2 + - - +
24C PHE* 4.1 18.2 - + - -
32C PHE* 4.4 3.4 - + - -
33C HIS* 3.1 4.9 - - - +
34C VAL* 2.8 44.8 + - + +
36C ILE* 5.9 0.2 - - + -
54C PHE* 3.7 29.8 - + - -
59C ALA* 3.5 35.2 - - + -
62C ASN* 4.1 14.8 - - + -
63C ILE* 3.9 9.4 - - + -
7D ALA* 4.0 4.3 - - + -
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Residues in contact with MET 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLN* 3.5 4.7 - - - +
10C ALA* 2.8 52.8 + - + +
21C GLU* 5.9 3.4 - - + +
22C PHE* 1.3 80.2 - - - +
24C PHE* 1.3 86.1 + - - +
25C ASP* 4.0 11.9 - - + +
30C GLU* 3.8 10.5 - - + +
32C PHE* 3.3 14.1 - - - +
33C HIS* 3.7 11.0 - - + +
136C VAL* 4.5 6.1 - - + -
137C PHE 4.6 11.7 - - - +
138C LEU* 3.7 23.6 - - + -
139C PRO* 3.6 31.2 - - + -
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Residues in contact with PHE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.0 22.9 - - + -
8C ILE 3.2 4.5 - - - -
9C GLN* 3.4 37.2 - - + -
22C PHE* 4.1 10.3 - + - -
23C MET* 1.3 89.6 - - - +
25C ASP* 1.3 60.1 + - - +
30C GLU* 3.4 0.2 - - - -
31C ILE* 2.9 28.0 + - + -
32C PHE* 3.0 42.8 + + + +
54C PHE* 5.0 0.9 - + - -
5D ILE* 3.8 16.6 - - + -
6D THR 3.8 20.6 - - - -
7D ALA* 4.8 2.5 - - + -
8D PHE* 5.1 4.9 - + - -
108D ASN* 4.0 11.4 - - - -
112D PHE* 4.1 22.2 - + - -
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Residues in contact with ASP 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C THR* 4.5 0.7 - - - +
7C ILE* 3.2 10.2 - - - +
8C ILE* 2.7 57.0 + - + +
23C MET* 4.0 13.6 - - + +
24C PHE* 1.3 77.4 - - - +
26C PHE* 1.3 63.2 + - - +
27C ASP 3.6 1.0 + - - -
28C GLY* 2.8 47.9 + - - +
29C ASP 3.1 10.8 + - - +
30C GLU 4.1 0.5 + - - -
31C ILE* 4.0 3.3 - - - +
138C LEU* 5.6 0.7 - - - +
139C PRO* 4.1 19.2 - - + +
146C ARG* 4.6 1.9 + - - -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C HIS* 3.4 37.0 - + + -
6C THR 3.5 2.5 - - - -
7C ILE* 3.8 28.0 - - + -
25C ASP* 1.3 72.3 - - - +
27C ASP* 1.3 82.9 + - - +
28C GLY 3.1 0.4 - - - -
29C ASP* 2.6 29.2 + - - +
31C ILE* 3.7 13.0 - - + +
109D TYR* 5.2 2.2 - + - -
112D PHE* 4.8 3.6 - + + -
116D LEU* 3.9 28.7 - - + -
117D VAL* 3.8 26.9 - - + -
149D TYR* 3.8 13.0 - + - -
179D TRP* 3.6 28.8 - + + -
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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