Contacts of the strand formed by residues 32 - 38 (chain D) in PDB entry 5GAG
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 ASN 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.3 31.3 - - + +
5D VAL* 2.9 37.5 + - - +
29D VAL* 3.4 12.5 - - - +
30D GLU 2.7 27.6 + - - -
31D ALA* 1.3 70.8 - - - +
33D ARG* 1.3 62.6 + - - +
34D VAL* 4.0 1.0 + - - +
50D VAL* 4.4 18.3 - - + +
51D THR 3.4 8.5 - - - +
52D THR* 4.5 4.1 - - - -
95D SER* 3.7 0.7 - - - -
96D ILE* 2.9 38.6 + - + +
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Residues in contact with ARG 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA* 3.7 11.1 + - + +
32D ASN* 1.3 73.9 - - - +
34D VAL* 1.3 61.9 + - - +
35D THR 3.6 1.4 + - - -
50D VAL* 3.2 4.3 - - - -
51D THR* 3.1 59.3 + - + +
52D THR* 3.6 12.7 - - - +
53D GLY 3.2 24.8 + - - -
73D VAL* 4.1 23.5 - - + +
74D GLU* 2.4 47.5 + - - +
75D ALA 3.7 4.4 + - - -
76D GLY* 3.8 0.8 - - - -
93D GLY 4.9 2.0 - - - +
94D GLN 4.0 4.0 - - - +
95D SER* 3.2 23.8 - - - +
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ARG* 1.3 73.2 - - - +
35D THR* 1.3 58.1 + - - +
36D GLN 3.9 13.7 - - - +
37D VAL* 4.0 17.7 - - + -
48D ILE* 4.1 16.2 - - + -
49D GLN 3.3 15.9 - - - +
50D VAL* 4.3 5.4 - - + -
73D VAL* 4.3 3.1 - - - +
90D PHE* 4.8 8.7 - - + -
91D THR 4.0 13.2 - - - +
92D VAL* 3.3 5.5 - - - +
93D GLY* 2.7 29.2 + - - +
94D GLN* 3.1 23.8 + - + +
96D ILE* 4.3 22.0 - - + -
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Residues in contact with THR 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ARG 3.6 0.6 + - - +
34D VAL* 1.3 73.5 - - - +
36D GLN* 1.3 61.7 + - - +
49D GLN* 2.4 41.8 + - - +
51D THR* 4.3 8.1 - - + +
67D HIS* 3.7 15.8 + - - +
68D PHE* 3.6 36.8 - - + -
70D LYS* 6.0 1.2 - - - +
71D ALA* 3.6 15.6 - - + +
73D VAL* 3.7 14.6 - - + -
79D LEU* 4.2 6.7 - - + +
92D VAL* 3.2 20.0 - - - +
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Residues in contact with GLN 36 (chain D).
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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2635A A 5.0 1.7 + - - -
2784A U 2.9 30.3 + - - +
2785A C 3.4 22.8 + - - +
34D VAL* 3.6 1.1 - - - +
35D THR* 1.3 83.3 + - - +
37D VAL* 1.3 70.6 + - - +
38D LYS* 3.4 35.0 + - + +
43D ASP* 4.2 0.8 + - - -
48D ILE* 3.7 0.5 - - - -
49D GLN* 2.9 52.8 + - + +
67D HIS* 4.1 14.3 - - + -
92D VAL* 3.8 2.0 - - - -
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D VAL* 4.0 14.4 - - + -
36D GLN* 1.3 83.4 - - - +
38D LYS* 1.3 67.7 + - - +
39D ASP* 3.9 10.1 + - + +
43D ASP* 4.6 1.4 - - - +
47D ALA 3.7 11.0 - - - +
48D ILE* 4.3 8.7 - - + -
84D LEU* 4.9 6.7 - - + -
90D PHE 3.6 28.3 - - - +
92D VAL* 3.7 26.1 - - + +
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Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2635A A 3.7 26.1 + - - -
2636A C 4.0 3.8 + - - -
2783A U 5.6 0.2 + - - -
2784A U 4.1 9.9 + - - -
36D GLN* 3.4 37.7 + - + +
37D VAL* 1.3 76.4 - - - +
39D ASP* 1.3 59.5 + - - +
43D ASP* 3.1 33.0 - - + +
45D TYR* 3.5 32.1 + - + +
46D ARG* 3.5 2.3 + - - +
47D ALA* 2.9 40.9 + - + +
49D GLN* 6.2 0.4 - - + -
81D GLU* 2.6 30.3 + - - +
84D LEU* 5.2 0.9 - - - +
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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