Contacts of the strand formed by residues 14 - 23 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B CYS* 3.6 1.7 - - - -
10B SER* 3.3 5.2 + - - -
11B TYR* 2.8 28.4 + + - +
12B LYS* 3.0 23.2 + - + -
13B GLY* 1.3 78.1 - - - +
15B CYS* 1.3 64.8 + - - +
16B TYR* 3.4 23.8 - - + +
49B GLU* 5.8 0.9 - - - -
122B LYS* 3.3 30.4 + - + +
123B TYR 3.5 9.2 + - - +
124B ARG* 3.4 40.4 - - + +
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Residues in contact with CYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B CYS* 2.0 47.6 - - + -
8B TRP* 3.7 9.0 - - + -
9B SER 3.0 5.6 - - - +
14B HIS* 1.3 73.9 - - - +
16B TYR* 1.3 63.5 + - - +
122B LYS* 3.2 7.6 - - - -
123B TYR* 2.9 63.6 + - + -
125B VAL* 3.3 22.9 - - - -
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Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP 4.6 0.3 - - - +
8B TRP* 3.7 2.6 - - - -
9B SER* 2.8 41.6 + - - +
11B TYR* 3.3 36.9 + + + -
14B HIS* 3.4 16.7 - - + +
15B CYS* 1.3 73.0 - - - +
17B LYS* 1.3 60.2 + - - +
42B MET* 5.0 0.4 - - + -
49B GLU* 2.6 39.6 + - + +
52B PHE* 3.3 24.2 - + - -
53B ILE* 4.4 19.1 - - + -
56B LEU* 3.8 18.3 - - + +
120B VAL* 4.3 9.4 - - + -
121B CYS 3.3 6.5 - - - +
122B LYS* 3.0 42.7 + - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP* 2.8 43.4 + - - +
8B TRP* 3.7 39.4 - - + +
16B TYR* 1.3 77.3 - - - +
18B VAL* 1.3 70.3 + - - +
19B PHE* 3.4 45.0 - - + -
56B LEU* 5.1 0.4 - - - -
120B VAL* 3.4 3.0 - - - -
121B CYS 3.0 31.0 + - - -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 1.3 83.6 - - - +
19B PHE* 1.3 65.8 + - - +
53B ILE* 5.0 1.3 - - + +
56B LEU* 4.3 19.4 - - + +
57B ALA* 3.8 36.1 - - + +
61B MET* 3.4 24.5 - - + +
63B ILE* 3.4 29.2 - - + -
66B VAL* 4.3 2.7 - - + -
119B PHE 3.4 11.9 - - - +
120B VAL* 3.7 21.3 - - + -
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TRP* 4.9 0.4 - + - -
17B LYS* 3.4 60.1 - - + -
18B VAL* 1.3 72.4 - - - +
20B LYS* 1.3 60.1 + - - +
21B VAL* 4.0 11.0 - - + +
22B GLU 4.5 0.2 + - - -
31B PHE* 3.6 21.3 - + - -
35B LEU* 3.6 21.3 - - + -
63B ILE* 3.9 3.4 - - - +
118B SER* 2.9 22.9 - - - -
119B PHE* 2.7 55.9 + + + +
121B CYS* 3.6 21.1 - - + -
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL 4.1 1.6 + - - -
19B PHE* 1.3 70.9 - - - +
21B VAL* 1.3 52.7 + - - +
22B GLU* 2.6 46.7 + - - +
61B MET* 3.5 26.2 - - + +
63B ILE* 3.7 14.9 - - + +
118B SER* 2.7 21.9 + - - +
686C GLN* 3.1 36.2 + - - +
689C GLU* 4.1 16.7 + - - -
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 4.0 11.7 - - + -
20B LYS* 1.3 75.8 - - - +
22B GLU* 1.3 71.8 + - - +
23B LYS* 4.2 22.0 - - - +
31B PHE* 5.8 3.4 - - + -
119B PHE* 3.3 35.7 - - + -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 2.6 39.6 + - - +
21B VAL* 1.3 86.2 - - - +
23B LYS* 1.3 61.5 + - - +
116B LYS* 2.8 48.5 - - + +
117B LYS* 3.5 14.4 - - - +
118B SER* 3.4 19.0 + - - +
673C LYS* 3.3 32.8 + - - -
674C ALA 4.6 2.1 - - - +
675C PHE* 5.2 2.3 - - - -
689C GLU* 4.7 4.6 - - - +
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 4.2 26.3 - - - +
22B GLU* 1.3 74.3 + - - +
24B THR* 1.3 70.3 + - - +
27B ASP* 3.5 39.9 - - + +
28B ALA* 4.0 2.9 - - - +
31B PHE* 3.9 27.7 - - + -
67B TRP* 3.0 6.1 + - - -
116B LYS* 3.6 9.6 - - - -
117B LYS 2.7 28.7 + - - +
119B PHE* 3.4 16.0 - - + -
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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