Contacts of the strand formed by residues 29 - 35 (chain B) in PDB entry 5IXG
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 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A HIS* 4.8 1.9 - - - +
122A SER* 5.7 1.8 - - - -
138A VAL 4.0 14.6 - - - -
139A ASP 5.4 0.7 - - - +
168A THR* 3.8 21.1 - - - +
169A ALA 4.3 0.4 - - - -
170A GLU* 2.5 32.4 + - - +
23B ASP* 3.9 5.9 - - - +
24B HIS* 3.0 33.2 + - - +
27B GLY* 3.3 2.9 - - - -
28B LEU* 1.3 82.6 + - - +
30B VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A SER* 5.7 0.7 - - - +
139A ASP* 3.7 36.5 + - + +
168A THR* 2.7 34.5 + - - +
21B GLU* 3.7 25.4 - - + +
22B ALA 3.6 8.1 - - - +
23B ASP* 5.9 1.1 - - - -
29B SER* 1.3 82.9 - - - +
31B TRP* 1.3 73.9 + - - +
32B ARG* 3.5 15.8 + - - +
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Residues in contact with TRP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER 3.4 17.7 - - - -
15A HIS* 3.4 26.6 - + - -
17A TYR* 3.8 19.1 - + - -
34A LYS* 4.5 1.8 - - - -
168A THR* 5.4 2.0 - - + -
20B PHE* 4.3 2.2 - + + -
21B GLU* 3.2 6.2 - - - -
22B ALA* 2.8 40.4 + - + +
23B ASP 4.2 9.4 - - - -
24B HIS* 3.8 29.3 - + + +
29B SER 4.2 0.8 + - - -
30B VAL* 1.3 71.2 - - - +
32B ARG* 1.3 64.5 + - - +
64B THR* 3.2 41.7 - - + -
66B SER* 4.2 8.7 - - - -
69B LEU* 3.6 22.9 - - + -
201B OTP 3.7 48.5 + - + +
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 3.7 33.0 - - - +
34A LYS* 2.7 31.9 + - - +
139A ASP* 2.7 42.2 + - - -
141A VAL* 6.1 0.8 - - - +
166A LEU* 3.8 38.0 + - - +
168A THR* 3.5 16.7 + - - +
20B PHE* 3.3 15.5 - - - +
21B GLU* 3.5 31.7 + - + -
30B VAL* 3.5 16.7 + - + +
31B TRP* 1.3 80.7 - - - +
33B GLY* 1.3 57.8 + - - +
64B THR* 3.5 6.6 - - - +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.0 5.2 - - - -
19B SER* 3.1 7.8 - - - -
20B PHE* 2.8 42.3 + - - -
32B ARG* 1.3 77.0 - - - +
34B LYS* 1.4 62.6 + - - +
63B HIS* 3.3 13.9 - - - -
64B THR* 4.5 0.4 - - - -
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 4.5 1.8 - - - -
32A ARG* 2.8 27.0 + - - +
33A GLY* 5.0 4.3 - - - -
63A HIS* 4.3 8.7 - - + +
64A THR 2.7 34.7 + - - +
65A GLY* 4.2 0.9 - - - +
17B TYR* 3.5 36.8 - - + +
18B PRO 3.4 13.9 - - - +
19B SER* 3.5 15.3 - - - +
20B PHE* 3.4 4.3 - - - -
33B GLY* 1.4 77.3 - - - +
35B PHE* 1.3 63.4 + - - +
36B ASP* 3.7 18.4 - - - +
62B ILE* 3.5 3.6 - - - +
63B HIS* 2.7 34.8 + - + +
168B THR* 5.7 1.4 + - - -
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.5 15.1 - - - +
18B PRO* 3.1 32.0 + - + +
20B PHE* 3.8 20.4 - + - -
34B LYS* 1.3 76.7 - - - +
36B ASP* 1.3 63.7 + - - +
37B LYS 3.4 0.7 + - - -
38B SER* 4.8 0.3 + - - -
57B THR* 3.4 25.8 - - + -
58B ASP 3.7 17.0 - - - -
59B ILE* 3.8 17.7 - - + -
61B SER* 3.6 5.2 - - - +
62B ILE* 3.5 39.5 - - + -
79B PHE* 3.9 13.7 - + - -
201B OTP 3.4 41.5 - - + -
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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