Contacts of the strand formed by residues 125 - 135 (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 LEU 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A TYR* 3.3 57.6 - - + +
65A GLY* 3.9 4.7 + - - -
66A GLY 5.1 0.3 + - - -
124A SER* 1.3 75.3 - - - +
126A ILE* 1.3 59.7 + - - +
127A ALA 3.4 22.7 - - - +
128A VAL* 4.1 9.9 - - + -
147A ASN* 4.1 8.3 - - + +
148A ILE 3.4 11.9 - - - +
149A TYR* 3.5 41.3 - - + +
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Residues in contact with ILE 126 (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* 4.3 15.3 - - + -
24A LEU* 4.7 7.4 - - + -
36A VAL* 4.5 18.2 - - + -
63A ALA* 3.7 2.1 - - - -
64A TYR 3.0 24.8 + - - +
66A GLY 5.7 0.9 - - - +
67A VAL* 3.5 34.1 - - + +
107A LEU* 5.3 3.8 - - + -
109A LEU* 5.4 0.7 - - + -
120A ILE* 3.9 29.8 - - + -
124A SER* 3.9 9.6 - - - +
125A LEU* 1.3 78.2 - - - +
127A ALA* 1.3 65.6 + - + +
148A ILE* 2.8 41.1 + - + +
149A TYR 4.6 0.4 - - - +
150A ALA* 3.9 6.1 - - + +
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Residues in contact with ALA 127 (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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62A SER 3.1 14.1 - - - +
64A TYR* 3.8 4.6 - - - -
84A PHE* 3.8 17.3 - - + -
107A LEU* 4.0 18.4 - - + -
125A LEU* 3.4 6.5 - - - +
126A ILE* 1.3 90.8 - - + +
128A VAL* 1.3 64.2 + - - +
129A LEU* 4.6 3.6 - - + -
148A ILE* 2.8 35.2 + - + -
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Residues in contact with VAL 128 (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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60A ARG 3.8 1.6 - - - +
61A GLY* 3.5 3.5 - - - -
62A SER* 3.0 32.8 + - - -
64A TYR* 3.3 33.9 - - + +
125A LEU* 4.1 12.1 - - + -
127A ALA* 1.3 78.7 - - - +
129A LEU* 1.3 62.2 + - - +
130A ILE* 4.6 10.4 - - + +
145A VAL* 3.7 21.1 - - + -
146A TRP 3.3 3.4 - - - +
147A ASN* 3.6 24.5 - - - +
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Residues in contact with LEU 129 (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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38A LEU* 3.9 34.3 - - + -
58A LEU* 4.2 9.2 - - + -
60A ARG 3.6 1.6 - - - -
61A GLY* 3.9 15.9 - - - -
75A VAL* 5.5 0.2 - - + -
84A PHE* 4.2 16.2 - - + -
103A TRP* 4.0 20.4 - - + -
105A VAL* 4.2 14.6 - - + -
107A LEU* 4.4 13.5 - - + -
127A ALA* 4.6 3.8 - - + -
128A VAL* 1.3 80.8 - - - +
130A ILE* 1.3 62.4 + - - +
146A TRP* 2.8 44.5 + - + +
148A ILE* 4.0 19.1 - - + -
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Residues in contact with ILE 130 (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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58A LEU* 3.6 5.1 - - - +
59A GLN* 2.8 53.8 + - - +
60A ARG* 2.9 60.4 + - + +
103A TRP* 4.1 3.4 - - - -
128A VAL* 4.6 9.4 - - + +
129A LEU* 1.3 74.9 - - - +
131A LEU* 1.3 67.7 + - - +
143A GLN* 3.9 21.1 - - + +
144A PHE 3.8 4.0 - - - +
145A VAL* 4.3 22.2 - - + -
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Residues in contact with LEU 131 (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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1A PHE* 4.0 11.2 - - + -
3A CYS* 4.0 1.8 - - - -
44A CYS* 3.7 27.6 - - - -
56A VAL* 3.4 25.1 - - + -
57A THR 3.4 4.3 - - - -
103A TRP* 3.5 38.3 - - + +
129A LEU 3.8 1.2 + - - -
130A ILE* 1.3 73.0 - - - +
132A ARG* 1.3 66.1 + - - +
133A GLN* 4.1 0.4 - - + -
142A PHE 3.7 0.2 - - - +
143A GLN* 3.4 3.1 - - - -
144A PHE* 2.7 64.5 + - + +
146A TRP* 3.6 13.2 - - - +
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Residues in contact with ARG 132 (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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55A TYR 3.5 1.2 - - - +
56A VAL* 3.3 5.4 - - - -
57A THR* 3.0 41.8 + - - +
59A GLN* 3.6 38.5 + - + +
89A GLU* 3.0 35.8 + - - -
130A ILE 3.7 0.8 + - - -
131A LEU* 1.3 74.3 - - - +
133A GLN* 1.3 62.2 + - - +
134A THR* 4.4 9.5 + - + +
141A ASP* 2.7 43.1 + - - +
142A PHE 3.4 6.5 - - - +
143A GLN* 4.6 1.1 - - + +
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Residues in contact with GLN 133 (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* 3.4 53.7 - - + +
54A ASP* 3.5 8.9 + - + +
55A TYR 3.3 7.4 - - - +
56A VAL* 4.4 1.6 - - + -
131A LEU* 4.1 3.8 + - + -
132A ARG* 1.3 74.0 - - - +
134A THR* 1.3 80.8 + - - +
135A ASN* 4.3 0.6 - - - +
140A ASP* 3.8 1.7 - - - +
141A ASP* 3.5 1.6 - - - -
142A PHE* 2.8 57.8 + - - +
144A PHE* 3.8 11.6 - - + -
1159A DEG 3.1 36.8 + - - -
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Residues in contact with THR 134 (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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54A ASP* 3.5 3.8 - - - -
55A TYR* 2.8 44.7 + - - +
92A ARG* 4.1 13.0 + - - +
132A ARG* 4.3 11.8 + - + +
133A GLN* 1.3 87.5 + - - +
135A ASN* 1.3 67.6 + - - +
140A ASP 3.5 17.7 - - - +
141A ASP* 3.7 25.6 - - + +
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Residues in contact with ASN 135 (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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52A ILE* 3.6 10.5 - - + -
53A THR 3.2 17.0 - - - +
54A ASP* 3.6 0.4 - - - +
55A TYR* 3.5 15.2 - - - -
92A ARG* 5.7 0.5 + - - -
133A GLN* 4.3 0.6 - - - +
134A THR* 1.3 80.4 + - - +
136A ASN* 1.3 58.7 + - - +
137A TYR* 2.7 22.0 + - - +
138A ASN* 2.8 44.7 + - - +
140A ASP* 3.8 5.8 + - - +
1159A DEG 2.9 33.3 + - - +
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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