Contacts of the strand formed by residues 123 - 129 (chain B) in PDB entry 6UWZ
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 PRO 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A VAL* 5.0 1.1 - - + -
100A PHE* 3.5 35.9 - - + -
149A TRP* 3.8 20.4 - - + +
56B VAL 3.5 5.6 - - - +
57B TRP* 3.7 16.6 - - + +
104B VAL* 3.8 1.2 - - - +
105B ALA* 3.0 19.4 + - - +
106B TYR* 3.3 37.8 + - + +
108B CYS* 4.3 0.2 - - - -
121B LEU 3.6 6.1 - - - +
122B PRO* 1.3 86.8 - - + +
124B ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 124 (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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100A PHE* 4.0 1.3 - - - -
55B ASN* 3.3 9.2 - - - +
56B VAL* 2.7 38.3 + - + +
58B MET* 5.0 0.7 - - + -
103B HIS 4.8 0.2 - - - +
104B VAL* 3.8 17.5 - - + -
105B ALA* 3.9 6.5 - - - +
122B PRO 4.9 0.7 - - - +
123B PRO* 1.3 77.7 - - - +
125B ILE* 1.3 63.5 + - - +
126B PHE* 3.6 38.1 - - + -
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Residues in contact with ILE 125 (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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95A ASN* 3.4 17.7 - - - +
96A ALA 3.9 11.4 - - - +
97A ASP* 3.6 22.9 - - - +
98A GLY 2.8 29.8 - - - +
100A PHE* 3.6 13.9 - - + -
53B THR* 4.5 7.6 - - + -
54B SER 3.3 7.6 - - - +
55B ASN* 4.5 4.3 - - + -
99B ASP* 4.9 0.5 - - - +
101B GLN* 4.5 13.3 - - - +
103B HIS 5.5 0.2 - - - +
105B ALA* 4.3 10.1 - - + +
124B ALA* 1.3 79.0 - - - +
126B PHE* 1.3 64.7 + - - +
127B ARG* 3.5 32.2 + - - +
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Residues in contact with PHE 126 (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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52B LEU 3.5 0.7 - - - +
53B THR* 3.4 5.4 - - - +
54B SER* 2.9 39.2 + - - +
56B VAL* 3.4 30.7 - - + -
58B MET* 4.1 3.1 - - - -
92B ILE 5.8 1.3 - - - -
94B LEU* 3.6 33.0 - - + -
99B ASP* 5.5 0.4 - - - -
101B GLN* 4.1 10.8 - - + -
102B TYR 4.2 4.9 - - - -
103B HIS* 3.5 30.1 - - - -
104B VAL* 4.5 6.5 - - + -
124B ALA* 3.6 16.6 - - + -
125B ILE* 1.3 79.3 - - - +
127B ARG* 1.3 64.3 + - - +
128B SER* 3.9 1.6 - - - +
146B LEU* 4.5 6.3 - - + -
148B PHE* 3.3 39.3 - + - -
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Residues in contact with ARG 127 (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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97A ASP* 4.1 30.5 + - - +
46B LYS* 5.7 4.6 - - - +
51B THR* 3.8 11.0 - - + +
52B LEU 3.2 4.3 - - - -
53B THR* 3.9 25.9 + - + +
94B LEU* 4.6 2.7 - - - +
97B ASN* 3.4 4.4 - - - -
98B ASN* 2.8 27.6 + - + +
99B ASP* 3.5 40.6 + - + +
101B GLN* 5.7 1.0 + - - +
125B ILE* 3.5 28.1 + - - +
126B PHE* 1.3 75.3 - - - +
128B SER* 1.3 61.5 + - - +
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Residues in contact with SER 128 (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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51B THR* 3.2 8.3 + - - -
52B LEU* 2.8 52.5 + - - +
94B LEU* 4.3 11.4 - - - -
96B ASN* 3.3 14.6 - - - -
97B ASN* 4.2 1.1 - - - +
98B ASN* 4.2 1.6 - - - -
126B PHE 3.9 1.4 - - - -
127B ARG* 1.3 75.7 - - - +
129B SER* 1.3 61.2 + - - +
130B CYS* 4.3 1.7 + - - +
145B SER 3.4 23.0 + - - -
146B LEU* 4.5 10.3 - - - -
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Residues in contact with SER 129 (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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50B GLU* 3.7 6.2 + - - +
96B ASN* 3.0 33.6 + - - +
97B ASN 5.0 0.9 - - - -
98B ASN* 3.1 29.3 + - - +
127B ARG 4.1 0.6 + - - -
128B SER* 1.3 71.6 - - - +
130B CYS* 1.3 60.5 + - - +
131B PRO* 4.3 4.0 - - - +
145B SER* 4.5 1.2 + - - +
39C ASN* 3.3 24.7 + - - -
41C LEU* 4.9 0.3 - - - +
181C THR* 5.0 10.3 + - - +
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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