Contacts of the strand formed by residues 20 - 27 (chain A) in PDB entry 3K57
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 GLU 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.1 7.4 - - - +
13A ARG* 2.9 80.6 + - + +
15A THR* 4.4 9.8 - - + +
18A GLY 3.3 1.9 + - - +
19A THR* 1.3 73.3 - - - +
21A VAL* 1.3 64.4 + - - +
22A SER* 4.8 8.9 + - - -
35A THR* 3.9 26.0 + - + +
36A LEU 5.1 2.2 - - - +
38A PRO* 5.2 2.5 - - - -
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A HIS 3.5 8.5 - - - +
12A TRP* 4.3 2.2 - - + -
19A THR* 3.8 3.7 + - + -
20A GLU* 1.3 78.5 - - - +
22A SER* 1.3 65.3 + - - +
23A PHE* 3.6 21.1 - - + -
35A THR* 3.7 3.2 - - - +
36A LEU* 2.9 58.3 + - + +
37A ALA 5.0 0.6 + - - -
39A GLN* 3.7 24.0 - - + -
110A PRO* 3.7 32.3 - - + +
111A PRO* 4.0 10.5 - - + -
114A TYR* 5.2 0.2 - - + -
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Residues in contact with SER 22 (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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11A HIS* 2.9 51.4 + - - +
20A GLU* 4.2 9.7 + - - +
21A VAL* 1.3 76.7 - - - +
23A PHE* 1.3 73.5 + - - +
24A TRP* 5.4 1.1 + - - -
33A GLN* 4.7 13.4 + - - -
34A VAL 3.2 12.6 - - - -
35A THR* 3.8 15.0 - - - -
270A LYS* 5.6 2.6 + - - -
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Residues in contact with PHE 23 (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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7A ILE* 4.3 7.9 - - + -
9A THR 3.5 6.1 - - - +
10A ARG* 3.8 23.8 - - + -
11A HIS* 4.7 0.2 - - - -
21A VAL* 3.6 29.4 - - + -
22A SER* 1.3 79.1 - - - +
24A TRP* 1.3 66.8 + - - +
25A LEU* 3.8 18.8 - - + -
32A LEU 3.7 1.2 - - - +
33A GLN* 3.5 2.6 - - - +
34A VAL* 2.8 40.9 + - + +
36A LEU* 4.1 18.6 - - + -
111A PRO* 3.9 16.4 - - + -
114A TYR* 4.3 9.0 - + - -
115A LEU* 3.5 39.3 - - + -
140A LEU* 4.1 15.9 - - + -
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Residues in contact with TRP 24 (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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7A ILE* 3.7 0.7 - - - -
8A LEU* 2.8 28.8 + - + -
9A THR* 3.1 18.9 + - - +
11A HIS* 3.5 25.6 - + - -
22A SER* 5.4 1.5 + - - -
23A PHE* 1.3 76.5 - - - +
25A LEU* 1.3 63.6 + - - +
31A PRO* 4.4 12.3 - - + -
32A LEU 3.6 4.5 - - - -
33A GLN* 3.6 56.5 - - + +
248A ARG* 3.8 41.1 - - + +
249A ASP* 4.1 22.9 - - + -
270A LYS* 3.1 24.8 - - + +
271A GLY* 3.5 16.6 - - - +
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Residues in contact with LEU 25 (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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5A GLY* 4.4 6.1 - - - -
6A PHE 3.4 10.5 - - - +
7A ILE* 3.7 24.5 - - + -
8A LEU* 4.7 4.2 - - - +
23A PHE* 3.8 18.8 - - + +
24A TRP* 1.3 81.2 - - - +
26A ALA* 1.3 60.2 + - - +
27A THR* 4.3 9.6 - - + -
30A GLY 3.8 0.2 - - - +
31A PRO* 3.4 6.1 - - - +
32A LEU* 2.8 45.3 + - + +
34A VAL* 4.1 15.5 - - + -
124A VAL* 3.7 27.6 - - + -
126A VAL* 4.0 26.0 - - + -
140A LEU* 4.5 4.7 - - + -
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Residues in contact with ALA 26 (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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5A GLY* 3.4 2.9 - - - -
6A PHE 2.8 37.5 + - - +
8A LEU* 4.0 14.9 - - + +
25A LEU* 1.3 72.3 - - - +
27A THR* 1.3 59.0 + - - +
30A GLY 4.3 3.4 - - - -
31A PRO* 4.9 1.3 - - - -
146A TYR* 3.7 6.2 - - - -
148A PRO* 3.6 23.3 - - + +
149A PRO 4.7 2.2 - - - +
150A LEU* 3.7 22.4 - - + -
218A ASP* 4.5 4.5 - - - +
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Residues in contact with THR 27 (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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3A GLN* 3.8 16.0 + - - +
4A ALA 3.8 19.1 - - - +
5A GLY* 4.3 4.5 - - - -
25A LEU* 4.1 4.0 - - + +
26A ALA* 1.3 78.6 - - - +
28A ASP* 1.3 63.8 + - - +
29A ASN* 2.9 17.8 + - - +
30A GLY* 2.7 37.1 + - - +
32A LEU* 3.8 27.3 - - + +
146A TYR* 3.2 11.0 - - - -
149A PRO* 3.8 14.8 - - - +
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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