Contacts of the strand formed by residues 26 - 33 (chain D) in PDB entry 3STJ
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 VAL 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D VAL 4.7 5.8 - - - +
23D LEU* 2.9 9.1 + - - +
24D PRO* 4.0 3.5 - - - +
25D ALA* 1.3 79.7 - - + +
27D VAL* 1.3 66.3 + - - +
67D GLY 3.4 14.4 - - - +
68D VAL* 4.7 3.6 - - + +
95D ASN 4.9 6.4 + - - -
127D ILE* 5.3 2.9 - - + -
144D VAL* 3.6 51.6 - - + +
145D GLY* 4.5 4.0 - - - +
152D GLN* 2.9 21.6 - - + +
189D GLY* 4.6 2.2 - - - -
190D ALA* 3.7 29.8 - - + +
192D LEU* 5.1 5.4 - - + -
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Residues in contact with VAL 27 (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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24D PRO 4.4 1.8 - - - +
25D ALA 4.0 0.2 - - - +
26D VAL* 1.3 80.5 - - - +
28D SER* 1.3 58.1 + - - +
29D VAL* 4.3 1.6 - - + -
66D SER* 3.3 8.7 + - - -
67D GLY* 2.8 52.8 + - - +
68D VAL 4.4 0.2 - - - +
69D ILE* 3.6 23.8 - - + -
77D VAL* 4.0 9.4 - - + -
92D ILE* 3.9 29.4 - - + -
93D GLN 3.6 9.4 - - - +
94D LEU* 3.5 29.8 - - + -
145D GLY 5.9 0.2 - - - -
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Residues in contact with SER 28 (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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27D VAL* 1.3 72.5 - - - +
29D VAL* 1.3 61.6 + - - +
30D ARG* 4.8 3.5 + - - +
64D LEU* 3.8 15.8 - - - +
65D GLY 3.7 5.2 - - - -
66D SER* 4.4 0.2 - - - +
91D SER 3.8 0.3 - - - +
92D ILE* 3.3 7.6 - - - +
93D GLN* 2.9 54.9 + - - +
146D ASN* 3.3 25.7 + - - -
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Residues in contact with VAL 29 (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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27D VAL* 4.3 1.1 - - + -
28D SER* 1.3 76.1 + - - +
30D ARG* 1.3 59.8 + - - +
31D VAL* 4.1 3.7 + - + +
63D GLY 4.0 0.3 - - - +
64D LEU* 3.5 4.9 - - - +
65D GLY 2.9 39.0 + - - +
66D SER 3.4 29.4 - - - +
67D GLY* 3.7 9.2 - - - +
77D VAL* 4.8 0.9 - - + -
79D THR* 4.3 3.8 - - - +
83D VAL* 4.0 10.2 - - + +
84D ILE* 3.7 30.7 - - + -
90D ILE* 4.0 15.5 - - + -
91D SER 3.6 2.9 - - - +
92D ILE* 4.0 16.2 - - + -
116D LEU* 4.4 5.2 - - + -
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Residues in contact with ARG 30 (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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28D SER* 4.0 4.2 + - - +
29D VAL* 1.3 72.8 - - - +
31D VAL* 1.3 67.2 + - - +
32D GLU* 5.2 9.5 + - + +
62D GLU* 3.1 35.9 + - + +
63D GLY 3.6 8.3 - - - +
64D LEU* 4.4 18.7 - - + +
89D LYS 4.0 0.2 - - - +
90D ILE* 3.5 4.3 - - - +
91D SER* 2.8 54.1 + - - +
93D GLN* 6.5 1.1 - - + -
99D GLU* 5.9 2.6 + - - -
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Residues in contact with VAL 31 (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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29D VAL* 4.2 7.0 - - + +
30D ARG* 1.3 80.7 - - - +
32D GLU* 1.3 65.5 + - - +
61D PHE* 3.7 24.5 - - + -
62D GLU* 3.3 6.6 - - - +
63D GLY* 2.8 39.7 + - - +
83D VAL* 3.7 26.2 - - + +
84D ILE* 3.9 19.5 - - + -
87D ALA* 3.7 31.6 - - + +
89D LYS 3.4 2.9 - - - -
90D ILE* 3.9 6.3 - - + -
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Residues in contact with GLU 32 (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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30D ARG* 5.2 10.8 + - + +
31D VAL* 1.3 82.6 - - - +
33D GLY* 1.3 52.3 + - - +
61D PHE 3.4 5.4 - - - +
62D GLU* 3.2 34.3 - - + +
87D ALA 3.7 0.2 - - - -
88D GLN* 2.8 30.7 + - - +
89D LYS* 2.9 44.7 + - + +
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Residues in contact with GLY 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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32D GLU* 1.3 75.5 - - - +
34D THR* 1.4 58.9 + - - -
60D PRO* 3.3 23.6 - - - +
61D PHE* 3.2 25.8 + - - +
86D GLN 3.7 9.6 - - - -
88D GLN* 3.7 19.5 - - - +
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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