Contacts of the strand formed by residues 16 - 21 (chain B) in PDB entry 2UZC
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 PHE 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 2.9 49.4 + - + +
8B LEU* 4.7 0.7 - - + -
14B TRP* 3.6 26.9 - + + -
15B GLY* 1.3 78.3 - - - +
17B ARG* 1.3 67.2 + - - +
18B LEU* 4.0 11.0 - - + -
30B ILE* 3.6 28.9 - - + -
32B SER 3.3 13.9 - - - +
33B LEU* 3.9 11.7 - - + -
39B ALA* 3.8 16.8 - - + -
70B ILE* 3.9 23.8 - - + -
77B LEU* 3.8 12.3 - - + -
79B MET* 3.8 23.1 - - + -
1089B EDO 3.5 9.9 + - - -
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Residues in contact with ARG 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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45A ARG* 3.4 42.5 - - - +
85A SER* 3.4 21.5 - - - +
86A ASP* 2.9 33.0 + - - +
87A LEU* 4.8 1.3 - - - -
16B PHE* 1.3 77.3 - - - +
18B LEU* 1.3 62.3 + - - +
30B ILE* 3.5 6.6 - - - -
31B SER* 2.9 35.0 + - - +
32B SER* 3.0 31.2 + - - +
1088B CL 3.0 25.1 - - + +
1089B EDO 3.6 10.8 + - - +
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Residues in contact with LEU 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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85A SER 5.2 0.4 + - - -
87A LEU* 4.1 10.3 - - + +
16B PHE* 4.0 8.5 - - + -
17B ARG* 1.3 76.1 - - - +
19B GLN* 1.3 62.9 + - - +
28B LEU* 4.5 10.3 - - + -
29B THR 3.2 24.0 - - - +
30B ILE* 3.9 12.3 - - + -
31B SER* 3.2 11.7 + - - -
50B VAL* 3.8 24.2 - - + -
53B ILE* 5.6 0.4 - - + -
63B HIS* 3.2 28.3 + - + +
66B ALA* 4.4 18.6 - - + -
67B GLN* 4.9 8.6 - - + +
70B ILE* 3.7 27.4 - - + -
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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 LEU* 1.3 74.9 - - - +
20B GLY* 1.3 64.3 + - - +
26B MET* 6.0 1.6 - - - +
27B PRO 3.6 0.4 - - - +
28B LEU* 3.4 5.7 - - - +
29B THR* 2.8 61.2 + - - +
31B SER* 4.0 11.1 - - - -
63B HIS* 3.9 6.3 - - - -
64D LEU* 3.6 33.4 - - - +
68D ASN* 5.4 5.5 + - - +
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Residues in contact with GLY 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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19B GLN* 1.3 78.8 - - - +
21B GLY* 1.3 59.4 + - - -
24B PHE* 3.4 16.5 - - - -
26B MET* 3.9 14.8 - - - -
27B PRO 3.5 10.3 - - - -
28B LEU* 3.6 3.2 - - - +
63B HIS* 2.9 31.5 + - - +
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Residues in contact with GLY 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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20B GLY* 1.3 73.7 - - - -
22B LYS* 1.3 68.1 + - - -
23B ASP* 3.2 7.6 - - - -
24B PHE* 3.0 12.3 + - - +
26B MET 2.9 28.7 + - - +
27B PRO 3.8 0.8 + - - -
28B LEU* 3.6 20.6 - - - +
61B MET 3.7 5.6 - - - -
63B HIS 4.1 1.6 - - - -
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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