Contacts of the strand formed by residues 29 - 35 (chain A) in PDB entry 4TNG
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 ALA 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASN 3.7 4.2 + - - -
28A VAL* 1.3 74.8 - - - +
30A VAL* 1.3 62.1 + - - +
31A HIS* 4.3 9.6 - - - +
47A GLY 3.6 7.2 - - - +
48A LYS* 4.3 18.2 - - + +
74A ASP* 2.9 54.8 + - + +
77A SER* 6.5 0.4 - - - -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.3 20.2 - - + -
16A VAL* 4.8 0.2 - - + -
28A VAL 3.8 10.8 - - - +
29A ALA* 1.3 79.2 - - - +
31A HIS* 1.3 66.6 + - - +
32A VAL* 4.5 6.1 - - + -
46A SER* 3.1 7.1 - - - -
47A GLY 2.9 31.7 + - - +
49A THR* 4.2 13.7 - - + -
55A LEU* 3.5 28.0 - - + -
71A VAL* 3.8 27.6 - - + -
72A GLU 3.4 4.5 - - - +
73A ILE* 4.4 13.2 - - + -
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.3 7.9 - - - +
30A VAL* 1.3 80.2 - - - +
32A VAL* 1.3 62.6 - - - +
33A PHE* 3.6 27.9 - + + -
45A ALA 3.8 3.1 - - - +
46A SER* 3.8 18.7 + - - -
70A LYS 3.6 1.0 - - - +
71A VAL* 3.5 1.4 - - - -
72A GLU* 2.7 46.7 + - + +
74A ASP* 3.6 29.7 + - - -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.2 16.2 - - + -
30A VAL* 4.5 6.7 - - + -
31A HIS* 1.3 77.6 - - - +
33A PHE* 1.3 67.9 + - - +
43A PRO* 3.8 1.7 - - - +
44A PHE* 2.8 48.0 + - + -
45A ALA* 2.7 28.5 + - + +
58A LEU* 4.0 31.4 - - + -
69A TYR* 4.4 8.5 - - + -
70A LYS 3.3 8.7 - - - +
71A VAL* 4.3 17.3 - - + -
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A HIS* 3.6 37.7 - + + -
32A VAL* 1.3 74.7 - - - +
34A ARG* 1.3 59.5 - - - +
41A TRP* 3.8 33.7 - - + -
42A GLU 3.2 8.7 - - - +
43A PRO* 3.7 35.2 - - + -
44A PHE* 4.1 4.0 - - - -
69A TYR* 3.2 8.5 - - - -
70A LYS* 2.8 52.4 + - + +
72A GLU* 4.0 24.2 - - + -
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 1.3 74.0 - - - +
35A LYS* 1.3 78.3 + - - +
36A ALA* 5.1 3.2 - - - +
41A TRP* 3.8 2.9 - - - -
42A GLU* 2.9 57.8 + - + +
44A PHE* 4.0 18.8 - - + +
65A VAL* 3.8 16.0 - - - +
66A GLU 3.0 23.0 + - - -
67A GLY* 4.0 7.4 - - - -
68A ILE 3.5 8.7 - - - +
69A TYR* 3.4 40.8 + - + -
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 1.3 91.4 + - - +
36A ALA* 1.4 69.6 + - - +
39A ASP* 3.0 41.2 + - - +
40A THR 3.6 10.5 - - - +
41A TRP* 3.6 23.6 - - + -
68A ILE* 2.9 54.6 + - + +
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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