Contacts of the strand formed by residues 14 - 23 (chain A) in PDB entry 1UEX
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 HIS 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A SER* 3.5 2.6 - - - -
11A TYR 2.8 34.9 + - - +
12A LYS* 3.3 40.4 + - + +
13A GLY* 1.3 81.6 + - - +
15A CYS* 1.3 64.9 + - - +
16A TYR* 3.7 18.8 - - + +
126A LYS* 3.3 32.5 + - + -
127A SER 3.2 18.1 + - - +
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Residues in contact with CYS 15 (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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4A CYS* 2.0 51.6 - - + -
8A TRP* 3.3 16.1 - - + -
9A SER 3.6 4.3 - - - +
10A SER* 4.3 2.0 - - - -
13A GLY 5.8 0.4 - - - -
14A HIS* 1.3 79.2 - - - +
16A TYR* 1.3 60.7 + - - +
126A LYS* 3.1 5.6 - - - -
127A SER* 2.9 40.5 + - - +
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Residues in contact with TYR 16 (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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8A TRP* 3.4 7.1 - - - +
9A SER* 2.8 39.3 + - - +
11A TYR* 3.3 32.4 - + + -
14A HIS* 3.7 25.2 - - + +
15A CYS* 1.3 73.0 - - - +
17A LYS* 1.3 65.5 + - - +
40A ALA* 4.5 7.6 - - + -
47A GLU* 3.0 32.9 + - + +
50A PHE* 3.5 28.5 - + - -
51A VAL* 4.3 19.5 - - + -
54A LEU* 3.5 17.7 - - + -
124A ILE* 4.6 3.4 - - + -
125A CYS 3.1 8.7 - - - +
126A LYS* 3.9 27.4 - - + -
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Residues in contact with LYS 17 (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 ASP* 2.8 53.4 + - - +
8A TRP* 3.2 30.7 - - + +
9A SER* 6.0 0.2 - - - -
16A TYR* 1.3 81.7 - - - +
18A VAL* 1.3 71.9 + - - +
19A PHE* 3.3 41.0 - - + -
54A LEU* 4.2 4.9 - - - +
124A ILE* 3.6 2.0 - - - +
125A CYS 3.3 25.6 + - - -
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Residues in contact with VAL 18 (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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17A LYS* 1.3 87.6 - - - +
19A PHE* 1.3 66.0 + - - +
20A LYS 4.0 1.2 + - - -
54A LEU* 3.7 29.3 - - + +
55A ALA* 3.9 11.9 - - + +
58A THR* 3.9 26.8 + - + +
59A LEU* 3.9 39.7 - - + -
122A PRO* 5.2 0.2 - - + -
123A PHE 3.5 11.0 - - - +
124A ILE* 4.0 22.4 - - + -
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Residues in contact with PHE 19 (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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8A TRP* 3.7 16.6 - + - -
17A LYS* 3.3 61.5 - - + -
18A VAL* 1.3 74.9 - - - +
20A LYS* 1.3 61.7 + - - +
21A LYS* 3.4 10.3 + - + +
31A PHE* 3.6 28.0 - + - -
35A ASN* 5.6 0.4 - - - -
122A PRO* 3.1 27.1 - - - +
123A PHE* 3.1 45.5 + + + +
125A CYS* 3.6 23.6 - - + -
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Residues in contact with LYS 20 (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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18A VAL* 4.0 1.8 + - - +
19A PHE* 1.3 70.0 - - - +
21A LYS* 1.3 67.6 + - + +
22A VAL* 3.4 8.7 + - - +
58A THR* 5.1 10.6 - - + +
59A LEU* 3.4 14.3 - - + +
61A LYS* 3.1 43.8 - - - +
64A TYR* 5.7 5.6 - - - -
122A PRO* 3.7 10.8 - - + +
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Residues in contact with LYS 21 (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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19A PHE* 3.2 13.4 - - + +
20A LYS* 1.3 79.8 - - + +
22A VAL* 1.3 64.2 + - - +
122A PRO* 3.7 1.7 - - - +
123A PHE* 3.5 21.7 - - + -
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Residues in contact with VAL 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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20A LYS* 4.1 8.7 - - - +
21A LYS* 1.3 80.1 - - - +
23A GLY* 1.3 58.6 + - - +
64A TYR* 4.3 17.9 - - + +
120A LYS* 3.4 49.1 - - + +
121A ASN 3.4 12.6 - - - -
122A PRO* 4.3 2.2 - - + -
123A PHE* 4.8 4.1 - - - -
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Residues in contact with GLY 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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22A VAL* 1.3 81.3 - - - +
24A THR* 1.3 70.1 + - - +
27A ASP* 4.5 11.2 - - - -
28A ALA* 4.5 3.2 - - - +
67A TRP* 3.1 17.7 + - - -
120A LYS* 3.8 15.1 - - - +
121A ASN 3.2 11.5 + - - +
123A PHE* 5.0 4.5 - - - -
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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