Contacts of the strand formed by residues 39 - 48 (chain A) in PDB entry 1DST
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLN* 3.1 4.3 - - - -
35A LEU* 2.7 42.5 + - + +
36A ASN 3.2 3.6 + - - +
38A GLY* 1.3 75.6 - - - +
40A HIS* 1.3 67.1 + - - +
41A LEU* 4.3 0.2 - - - -
151A ARG* 6.0 3.8 - - - +
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Residues in contact with HIS 40 (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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32A SER* 2.7 28.2 + - - +
33A VAL 4.0 2.9 - - - -
34A GLN* 4.2 4.3 + - - -
38A GLY 3.9 1.6 + - - -
39A ALA* 1.3 74.8 - - - +
41A LEU* 1.3 60.9 + - - +
42A CYS 3.2 27.9 + - - -
43A GLY* 3.9 3.6 - - - -
73A LEU* 3.9 22.4 - - + +
141A TRP* 3.7 50.1 + + + +
151A ARG* 4.9 10.8 + - - -
193A GLY* 2.9 29.3 + - - -
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Residues in contact with LEU 41 (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 VAL* 2.8 24.7 + - + +
35A LEU* 4.0 44.4 - - + +
39A ALA 3.3 0.6 + - - -
40A HIS* 1.3 78.5 - - - +
42A CYS* 1.3 72.5 + - - +
58A CYS* 3.5 28.3 - - + +
61A ASP* 4.3 26.5 - - + +
64A VAL* 5.0 5.2 - - + -
192A LYS* 5.5 9.6 + - - +
193A GLY* 3.9 15.6 - - - -
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Residues in contact with CYS 42 (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 VAL* 2.7 38.8 + - + -
40A HIS* 3.2 11.2 + - - -
41A LEU* 1.3 91.6 - - + +
43A GLY* 1.3 63.0 + - - +
54A SER* 4.2 2.2 - - - +
57A HIS* 5.1 0.9 - - - -
58A CYS* 2.0 54.5 - - + -
61A ASP* 5.0 4.7 - - - -
193A GLY* 3.9 6.5 - - - -
195A SER* 3.2 15.9 - - - +
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Residues in contact with GLY 43 (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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30A MET* 4.5 7.4 - - - -
31A ALA 3.7 8.5 - - - -
33A VAL* 3.6 3.1 - - - +
40A HIS* 4.2 6.3 - - - -
42A CYS* 1.3 76.7 - - - +
44A GLY* 1.3 52.0 + - - -
54A SER* 2.8 27.7 + - - -
140A GLY* 6.0 1.6 - - - -
193A GLY 3.7 7.3 + - - -
194A ASP 4.8 1.3 - - - -
195A SER 2.8 12.2 + - - -
196A GLY* 3.3 10.8 - - - -
197A GLY* 3.9 10.3 - - - -
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Residues in contact with GLY 44 (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 TYR 3.9 1.2 - - - +
30A MET* 4.0 3.7 - - - +
31A ALA* 3.1 37.7 + - - +
33A VAL* 4.4 1.6 - - - -
43A GLY* 1.3 74.5 - - - -
45A VAL* 1.3 65.9 + - - +
52A VAL* 4.1 7.9 - - - -
53A LEU 3.2 12.3 - - - -
54A SER* 4.2 1.1 - - - -
196A GLY 3.3 5.2 + - - -
197A GLY* 4.1 1.6 - - - -
198A PRO* 4.0 5.9 - - - +
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Residues in contact with VAL 45 (chain A).
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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29A TYR* 3.5 23.8 - - + +
44A GLY* 1.3 76.6 - - - -
46A LEU* 1.3 74.1 + - - +
47A VAL* 3.1 5.4 + - + -
52A VAL* 3.4 5.3 - - - +
53A LEU* 2.7 48.1 + - + +
123A LEU* 4.4 8.3 - - + -
196A GLY 4.1 3.8 - - - +
197A GLY 4.3 0.2 - - - -
198A PRO* 3.5 37.0 - - + -
209A LEU* 4.2 27.6 - - + -
212A VAL* 5.5 2.2 - - + -
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Residues in contact with LEU 46 (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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28A PRO 4.8 1.6 - - - +
29A TYR* 2.9 21.5 + - - +
31A ALA* 4.9 0.4 - - - +
44A GLY 4.4 0.2 - - - -
45A VAL* 1.3 75.1 - - - +
47A VAL* 1.3 58.4 + - - +
48A ALA 3.2 23.6 - - - +
49A GLU 4.5 3.4 - - - +
51A TRP 3.6 8.3 - - - +
52A VAL* 4.0 13.8 - - + +
68A LEU* 4.0 26.7 - - + -
108A LEU* 4.3 8.1 - - + -
112A ALA* 4.6 0.4 - - + -
114A LEU* 4.4 6.5 - - + -
120A VAL* 3.7 29.6 - - + -
121A ARG 3.9 20.2 - - - +
122A PRO* 3.2 9.4 - - + +
123A LEU 3.1 23.7 + - - -
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Residues in contact with VAL 47 (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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45A VAL* 3.1 21.0 + - + +
46A LEU* 1.3 75.6 - - - +
48A ALA* 1.3 65.2 + - + +
51A TRP* 3.1 25.3 + - + +
53A LEU* 4.0 30.7 - - + +
105A LEU* 4.2 9.0 - - + -
122A PRO* 3.9 9.4 - - - +
123A LEU 4.3 9.0 - - - +
124A TRP* 3.9 35.5 + - - +
209A LEU* 4.4 4.5 - - + -
238A ILE* 5.5 3.4 - - + -
242A LEU* 5.0 10.3 - - + +
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Residues in contact with ALA 48 (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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46A LEU* 3.2 21.4 - - - +
47A VAL* 1.3 79.7 - - - +
49A GLU* 1.3 67.1 + - - +
50A GLN 3.1 2.1 + - - -
51A TRP* 3.3 31.7 + - + -
122A PRO* 4.0 13.2 - - - +
242A LEU* 4.8 12.1 - - + -
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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