Contacts of the strand formed by residues 17 - 22 (chain B) in PDB entry 1UK3
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 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.7 18.2 - - - +
14B GLU* 3.5 12.6 + - - +
15B GLY 5.0 1.0 - - - -
16B CYS* 1.3 84.2 + - - +
18B VAL* 1.3 66.2 + - - +
28B ASN* 4.0 11.2 - - + -
29B GLY 3.4 18.8 - - - +
30B LEU* 4.1 12.6 - - - -
70B ALA* 5.0 3.5 - - - -
115B LEU* 4.0 8.3 - - + -
117B CYS* 3.5 32.5 - - + -
120B GLY 3.7 18.8 - - - +
122B PRO* 4.3 4.0 - - + -
146B GLY 3.8 20.9 - - - +
147B SER* 4.7 3.1 - - - -
148B VAL* 4.3 16.2 - - + +
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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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16B CYS 4.3 0.2 - - - +
17B MET* 1.3 79.2 - - - +
19B GLN* 1.3 62.4 + - - +
20B VAL* 4.4 4.5 - - + -
28B ASN* 3.6 1.0 - - - +
29B GLY* 3.0 34.1 + - - +
30B LEU 4.4 0.2 - - - +
31B TRP* 3.7 37.0 - - + -
36B VAL* 3.7 31.6 - - + -
68B VAL* 5.0 3.6 - - + -
69B GLN 3.7 12.8 - - - +
70B ALA* 4.0 14.6 - - + +
71B GLY 5.1 0.9 - - - +
75B LEU* 5.0 3.8 - - + -
120B GLY* 3.3 18.5 - - - -
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Residues in contact with GLN 19 (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* 1.3 75.6 - - - +
20B VAL* 1.3 62.3 + - - +
21B THR* 4.6 1.3 - - - +
26B THR* 3.4 31.9 - - + +
27B LEU 3.6 2.9 - - - +
67B LEU 3.3 1.5 - - - +
68B VAL* 2.9 8.3 - - - +
69B GLN* 2.8 75.2 + - + +
71B GLY 5.6 0.9 - - - +
119B ASN* 2.7 35.5 + - - +
120B GLY* 4.2 2.2 - - - -
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Residues in contact with VAL 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* 4.4 0.7 - - + -
19B GLN* 1.3 79.8 - - - +
21B THR* 1.3 69.3 + - - +
25B THR 3.7 0.7 - - - +
26B THR* 3.3 2.3 - - - -
27B LEU* 2.9 43.6 + - + +
29B GLY* 3.9 16.2 - - - +
36B VAL* 3.8 29.2 - - + -
38B CYS* 4.1 20.6 - - - -
42B VAL* 4.2 14.6 - - + +
66B PHE* 4.9 5.2 - - + -
67B LEU 3.4 2.9 - - - +
68B VAL* 4.0 8.1 - - + -
89B LEU* 4.1 17.7 - - + -
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Residues in contact with THR 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 GLN* 4.6 0.9 + - - +
20B VAL* 1.3 77.7 - - - +
22B CYS* 1.3 64.0 + - - +
23B GLY 3.3 20.2 - - - +
24B THR 5.0 0.7 - - - -
25B THR 3.1 11.9 - - - +
26B THR* 2.5 30.7 + - - +
65B SER 3.8 0.9 - - - +
66B PHE* 3.5 6.1 - - - +
67B LEU* 2.8 55.7 + - + +
69B GLN* 4.5 8.5 + - - -
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Residues in contact with CYS 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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21B THR* 1.3 74.5 - - - +
23B GLY* 1.3 68.8 + - - +
24B THR 3.1 0.7 + - - -
25B THR* 2.9 25.9 + - - +
42B VAL* 3.5 24.6 - - + +
43B ILE* 4.1 7.0 - - - -
45B THR* 5.5 0.7 + - - -
61B LYS* 3.4 34.3 - - - -
65B SER* 3.7 14.6 - - - -
66B PHE* 3.6 28.3 - - + -
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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