Contacts of the strand formed by residues 34 - 39 (chain D) in PDB entry 1KXT
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 MET 34 (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* 4.3 17.9 - - + -
22D CYS* 5.5 3.1 - - - +
24D ALA* 5.1 7.9 - - + -
28D THR* 6.3 1.8 - - - -
29D PHE 4.2 10.3 - - - +
30D SER* 3.9 32.3 - - - -
32D TYR* 3.1 14.4 + - + +
33D PRO* 1.3 74.1 - - - +
35D GLY* 1.3 59.2 + - - +
36D TRP* 5.9 0.2 - - - -
50D ARG* 3.6 4.6 - - - +
51D ILE* 3.1 42.1 + - + +
69D ILE* 5.0 0.9 - - - +
71D ARG* 4.6 4.5 - - - +
76D ASN 5.8 3.8 - - - +
77D THR* 6.2 1.1 - - - -
78D ALA* 4.9 24.5 - - + +
92D CYS* 5.4 4.5 - - - -
93D ALA 3.7 4.9 - - - +
94D ALA* 3.2 29.4 - - + -
95D GLY 4.8 1.1 - - - +
100D PRO* 5.5 0.9 - - - -
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Residues in contact with GLY 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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34D MET* 1.3 75.6 - - - +
36D TRP* 1.3 67.5 + - - -
37D TYR* 4.2 10.1 - - - -
47D LEU* 5.1 0.2 - - - -
49D ALA 3.6 11.0 - - - -
50D ARG* 4.3 5.2 - - - -
92D CYS* 4.1 0.8 - - - -
93D ALA* 2.7 52.5 + - - +
94D ALA* 4.5 0.2 - - - +
100D PRO* 4.9 3.7 - - - -
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Residues in contact with TRP 36 (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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6D ALA* 4.2 8.5 - - + -
20D LEU* 3.6 45.3 - - + -
21D SER 3.5 28.0 - - - -
22D CYS* 3.6 11.9 - - + -
35D GLY* 1.3 76.3 - - - -
37D TYR* 1.3 65.4 + - - +
47D LEU* 3.3 8.7 - - - +
48D SER* 2.8 29.2 + - - -
49D ALA* 3.2 9.0 + - + +
69D ILE* 3.9 22.5 - - + +
78D ALA* 3.8 22.6 - - + +
79D TYR 3.5 19.6 + - - +
80D LEU* 3.7 29.8 - - + -
90D TYR* 4.9 5.8 - - + -
91D TYR 3.6 7.0 - - - -
92D CYS* 4.0 26.0 - - + -
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Residues in contact with TYR 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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270C SER* 3.8 15.0 - - - -
272C GLU* 4.5 11.5 + - - -
35D GLY* 3.9 10.8 - - - -
36D TRP* 1.3 79.2 - - - +
38D ARG* 1.3 62.3 + - - +
45D CYS* 4.2 9.4 - - - -
46D GLU 3.2 8.5 - - - +
47D LEU* 3.6 35.8 - - + +
48D SER* 4.0 3.4 - - - +
50D ARG* 4.6 5.2 + - - -
90D TYR* 3.4 8.8 - - - +
91D TYR* 3.0 38.6 + - + +
93D ALA* 4.0 11.4 - - + -
100D CYS* 3.2 80.7 + + - -
103D TRP* 5.4 0.9 - + - -
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Residues in contact with ARG 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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37D TYR* 1.3 77.3 - - - +
39D GLN* 1.3 61.1 + - - +
40D ALA* 4.2 1.6 + - + +
44D GLU 4.2 1.4 - - - +
45D CYS* 4.0 0.7 - - - -
46D GLU* 2.9 62.1 + - + +
48D SER* 5.2 7.5 + - - +
62D SER* 3.5 23.0 + - - -
63D VAL* 4.1 17.2 - - - +
67D PHE* 4.1 2.2 - - - -
85D GLU* 5.0 6.0 + - - +
86D ASP* 2.8 36.6 + - - +
88D ALA* 4.1 10.3 - - + -
89D VAL 3.2 8.1 - - - +
90D TYR* 3.0 46.6 + - + -
91D TYR* 5.0 0.7 - - - -
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Residues in contact with GLN 39 (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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38D ARG* 1.3 72.6 - - - +
40D ALA* 1.3 71.4 + - - +
41D PRO* 4.1 0.5 - - - +
43D LYS 2.8 27.5 + - - +
44D GLU 4.6 1.3 - - - -
45D CYS* 3.9 34.1 - - + +
88D ALA* 3.4 4.3 - - - +
89D VAL* 2.8 32.6 + - + +
91D TYR* 3.6 25.3 - - + +
100D VAL* 3.2 58.0 + - + +
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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