Contacts of the strand formed by residues 142 - 150 (chain A) in PDB entry 1UWF
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.9 2.7 - - + -
14A GLY* 3.3 51.4 - - - +
131A LEU 3.7 0.5 - - - +
132A ARG* 3.4 5.0 - - - +
133A GLN* 2.8 56.3 + - - +
140A ASP* 3.4 42.8 - - + -
141A ASP* 1.3 84.4 + - - +
143A GLN* 1.3 64.9 + - - +
144A PHE* 4.0 10.9 + - + -
1159A DEG 3.7 8.7 - - - -
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Residues in contact with GLN 143 (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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14A GLY 4.9 0.8 + - - -
15A GLY* 3.4 1.4 - - - -
16A GLY* 2.9 26.0 + - - +
59A GLN* 2.7 39.8 + - - +
60A ARG* 4.5 7.1 - - - +
130A ILE* 3.9 23.5 - - + +
131A LEU 3.4 3.1 - - - -
132A ARG* 4.9 2.2 - - + -
141A ASP* 5.6 2.5 - - - +
142A PHE* 1.3 77.4 - - - +
144A PHE* 1.3 62.2 + - - +
145A VAL* 3.8 9.8 - - + +
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Residues in contact with PHE 144 (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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1A PHE* 3.6 31.2 - + - -
2A ALA* 4.1 8.7 - - - -
3A CYS* 3.9 13.5 - - - -
11A ILE* 3.3 38.1 - - + -
12A PRO 3.5 18.6 - - - -
14A GLY 4.5 0.9 - - - -
15A GLY* 3.5 21.3 - - - -
16A GLY 3.6 3.8 - - - -
130A ILE* 4.7 0.2 - - - -
131A LEU* 2.7 57.1 + - + +
133A GLN* 3.8 16.2 - - + -
142A PHE* 4.0 9.6 - - + -
143A GLN* 1.3 73.5 - - - +
145A VAL* 1.3 61.3 + - - +
146A TRP* 3.2 26.1 - - + +
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Residues in contact with VAL 145 (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 ILE* 4.0 1.7 - - - +
16A GLY 2.8 19.7 + - - +
17A SER* 3.2 10.2 - - - -
18A ALA 3.0 27.7 + - - +
128A VAL* 3.7 26.7 - - + -
129A LEU 3.9 2.7 - - - -
130A ILE* 4.3 19.5 - - + +
143A GLN* 4.5 16.4 - - + +
144A PHE* 1.3 72.1 - - - +
146A TRP* 1.3 61.6 + - - +
147A ASN* 3.7 12.5 + - - +
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Residues in contact with TRP 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A CYS* 3.5 37.5 - - + -
4A LYS* 4.4 7.0 - - - -
5A THR* 3.6 24.5 - - + -
9A THR 5.1 0.7 - - - -
11A ILE* 3.6 28.7 - - + -
18A ALA* 3.5 15.9 - - + -
20A VAL* 3.7 17.7 - - + -
42A ILE* 3.5 32.8 - - + -
103A TRP* 3.4 24.9 - + - -
128A VAL* 3.3 4.0 - - - -
129A LEU* 2.8 45.3 + - + +
131A LEU* 3.6 16.8 - - - +
144A PHE* 3.2 24.8 + - + +
145A VAL* 1.3 72.0 - - - +
147A ASN* 1.3 63.9 + - - +
148A ILE* 3.6 12.8 + - + +
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Residues in contact with ASN 147 (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 SER* 4.4 16.0 + - - -
18A ALA 2.9 14.3 + - - +
19A ASN* 3.3 25.8 + - - +
20A VAL 2.8 26.5 + - - +
125A LEU* 4.1 6.1 - - + -
127A ALA 3.8 4.0 - - - -
128A VAL* 3.6 26.3 - - - +
145A VAL* 3.7 7.6 + - - +
146A TRP* 1.3 71.6 - - - +
148A ILE* 1.3 63.1 + - - +
149A TYR* 3.6 16.3 + - + +
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.5 28.7 - - + +
22A VAL* 4.1 21.5 - - + -
36A VAL* 4.5 4.7 - - + -
38A LEU* 3.9 19.7 - - + -
42A ILE* 4.8 0.2 - - + -
107A LEU* 5.6 1.6 - - + -
125A LEU* 3.4 4.5 - - - +
126A ILE* 2.8 52.0 + - + +
127A ALA* 2.8 24.7 + - + +
129A LEU* 4.0 20.2 - - + -
146A TRP* 3.9 17.5 - - + +
147A ASN* 1.3 74.2 - - - +
149A TYR* 1.3 62.8 + - - +
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Residues in contact with TYR 149 (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 ASN* 3.7 34.8 + - + -
20A VAL 2.8 8.5 + - - -
21A TYR* 3.5 28.6 - + + -
22A VAL* 2.9 31.5 + - - +
123A GLY* 3.3 23.6 - - - +
124A SER* 3.4 0.9 - - - -
125A LEU* 3.5 39.2 - - + +
126A ILE* 4.8 1.3 - - - -
147A ASN* 3.6 24.1 + - + +
148A ILE* 1.3 74.7 - - - +
150A ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 150 (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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21A TYR* 5.6 0.7 - - - -
22A VAL* 3.8 5.8 - - - -
24A LEU* 3.5 26.9 - - + -
120A ILE* 3.7 21.1 - - + -
121A LYS 4.1 4.9 - - - +
123A GLY* 2.6 33.8 + - - -
124A SER 3.0 14.0 + - - +
126A ILE* 3.9 6.5 - - + +
148A ILE 4.3 0.2 + - - -
149A TYR* 1.3 73.1 - - - +
151A ASN* 1.3 58.1 + - - +
152A ASN 4.0 7.0 - - - +
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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