Contacts of the strand formed by residues 17 - 25 (chain E) in PDB entry 5YL4
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 17 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A ASP 5.6 1.3 - - - -
355A ILE 3.3 13.2 - - - -
357A TYR* 3.4 18.9 + - - -
13E LYS* 4.6 0.2 - - - +
14E CYS* 2.8 36.8 + - - +
15E THR 3.5 2.2 - - - -
16E SER* 1.3 81.9 + - - +
18E GLN* 1.3 63.5 + - - +
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Residues in contact with GLN 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ALA 6.2 0.2 - - - -
324A VAL* 4.7 5.9 - - - +
325A PRO* 3.2 42.5 - - + +
355A ILE* 2.7 50.5 + - + +
357A TYR* 2.7 28.7 + - + +
11E LEU* 3.5 16.8 - - + +
12E ASN 3.3 14.8 - - - +
13E LYS* 3.6 27.5 - - + +
14E CYS* 5.6 0.2 - - - -
17E GLY* 1.3 74.5 - - - +
19E SER* 1.3 58.4 + - - +
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ALA* 3.5 30.3 + - - +
248A LEU* 3.8 21.9 + - - -
353A VAL 3.2 15.5 - - - -
354A GLY* 4.1 3.1 - - - -
10E GLU 3.7 1.7 + - - +
11E LEU* 3.5 2.8 - - - +
12E ASN* 3.0 33.4 + - - +
18E GLN* 1.3 76.2 - - - +
20E PHE* 1.3 69.8 + - - +
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Residues in contact with PHE 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU* 5.3 0.7 - - - +
325A PRO* 3.5 45.8 - - + -
328A VAL* 4.1 4.9 - - + -
329A ASN* 3.3 25.4 - - - -
352A LYS* 3.6 3.5 - - - +
353A VAL* 2.7 75.7 + - + +
355A ILE* 4.1 7.9 - - + -
8E VAL* 4.0 14.4 - - + -
9E ILE 3.7 13.7 - - - +
10E GLU* 4.0 6.1 - - - -
11E LEU* 4.1 15.0 - - + -
18E GLN 5.2 0.2 - - - -
19E SER* 1.3 82.4 - - - +
21E GLU* 1.3 69.4 + - - +
22E VAL* 4.5 3.8 - - + -
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Residues in contact with GLU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A PRO* 5.3 5.9 - - - +
350A GLY* 5.8 0.6 - - - -
351A PHE 3.5 13.5 - - - +
352A LYS* 3.5 40.3 + - + +
7E GLU 3.9 0.2 - - - +
8E VAL* 3.6 4.0 - - - -
9E ILE* 3.0 54.6 + - + +
10E GLU* 4.9 7.6 + - + +
20E PHE* 1.3 79.7 - - - +
22E VAL* 1.3 63.6 + - - +
23E ILE* 3.3 29.9 - - + +
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ASN* 4.1 18.4 - - - +
332A ILE* 3.8 30.1 - - + -
350A GLY* 3.2 2.4 - - - -
351A PHE* 2.9 54.3 + - + +
353A VAL* 4.5 5.8 - - + -
6E MET* 3.5 36.1 - - + -
7E GLU 3.5 8.7 - - - +
8E VAL* 4.4 7.9 - - + -
20E PHE* 4.5 3.1 - - + -
21E GLU* 1.3 75.1 - - - +
23E ILE* 1.3 61.2 + - - +
24E LEU* 3.9 3.6 + - + +
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Residues in contact with ILE 23 (chain E).
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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348A PRO* 4.5 17.7 - - + -
349A THR 3.7 4.9 - - - +
350A GLY* 4.1 3.8 - - - -
6E MET* 4.0 2.1 - - - -
7E GLU* 3.3 33.0 + - + +
9E ILE* 4.0 21.3 - - + -
21E GLU* 3.3 30.1 - - + +
22E VAL* 1.3 75.8 - - - +
24E LEU* 1.3 61.7 + - - +
25E LYS* 3.5 30.1 - - - +
26E PRO* 4.3 5.4 - - + -
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ILE* 4.0 12.1 - - + -
336A LYS* 3.7 44.2 - - + -
341A ILE* 6.3 0.4 - - + -
349A THR* 2.9 24.4 + - + +
350A GLY* 4.9 0.2 - - - -
351A PHE* 4.2 25.6 - - + -
6E MET* 3.6 49.7 + - + +
22E VAL* 4.5 6.1 - - + +
23E ILE* 1.3 73.3 - - - +
25E LYS* 1.3 62.6 + - + +
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Residues in contact with LYS 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A THR* 2.9 47.6 + - + +
23E ILE* 3.4 10.4 - - - +
24E LEU* 1.3 81.3 - - + +
26E PRO* 1.4 95.0 + - + +
27E PRO 3.8 14.5 + - - -
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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