Contacts of the strand formed by residues 115 - 121 (chain A) in PDB entry 2UYC
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 VAL 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASP 2.8 5.7 + - - +
74A ILE* 3.2 18.4 - - + -
75A LEU 2.8 25.6 + - - -
113A PRO* 3.7 3.5 - - - +
114A LYS* 1.3 86.8 - - + +
116A VAL* 1.3 78.7 + - - +
169A ILE* 4.0 18.6 - - + -
170A CYS 3.2 10.3 - - - +
171A PHE* 3.7 23.8 - - + -
318A ILE* 3.9 24.9 - - + -
322A LEU* 4.0 16.8 - - + -
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Residues in contact with VAL 116 (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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75A LEU* 3.5 18.6 - - + -
104A ILE* 4.5 0.9 - - + -
108A VAL* 3.8 25.8 - - + -
113A PRO* 4.0 8.1 - - + -
115A VAL* 1.3 78.9 - - - +
117A PHE* 1.3 60.3 + - - +
118A MET* 3.9 33.9 - - + -
140A MET* 3.8 16.4 - - + -
145A TYR* 3.9 16.6 - - + -
168A MET 3.4 4.3 - - - +
169A ILE* 3.5 1.0 - - - -
170A CYS* 2.8 46.6 + - + +
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Residues in contact with PHE 117 (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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24A PHE* 3.8 27.1 - + - -
28A LEU* 4.4 17.7 - - + -
74A ILE* 4.4 11.0 - - + -
75A LEU 2.8 12.9 + - - +
76A CYS* 3.4 5.6 - - - -
77A ALA 2.9 23.9 + - - -
115A VAL* 4.1 0.4 - - + -
116A VAL* 1.3 72.4 - - - +
118A MET* 1.3 70.1 + - - +
167A TYR* 4.2 6.5 - + - -
168A MET 3.5 1.3 - - - -
169A ILE* 3.2 27.4 - - + -
311A LEU* 3.7 31.0 - - + -
314A ILE* 3.3 35.0 - - + -
315A ALA* 4.5 2.0 - - - -
318A ILE* 3.9 20.2 - - + -
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Residues in contact with MET 118 (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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24A PHE* 4.6 0.4 - - - -
77A ALA* 3.2 20.4 - - + +
79A PHE* 3.9 12.8 - - + -
101A PHE* 3.7 39.0 - - + -
104A ILE* 3.9 17.5 - - + -
116A VAL* 3.9 21.5 - - + -
117A PHE* 1.3 83.6 - - - +
119A GLU* 1.3 64.5 + - - +
136A VAL* 4.0 14.4 - - + -
140A MET* 4.2 4.0 - - - -
167A TYR* 3.6 3.3 - - - -
168A MET* 2.9 44.5 + - + +
170A CYS* 4.1 19.5 - - - -
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Residues in contact with GLU 119 (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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24A PHE* 3.7 18.2 - - + -
77A ALA 3.1 4.4 + - - -
78A GLY* 3.2 20.0 - - - -
79A PHE* 3.5 11.1 + - - -
118A MET* 1.3 78.7 - - - +
120A ASN* 1.3 67.2 + - - +
165A ARG* 3.3 22.9 + - + +
166A ILE 3.5 7.6 - - - +
167A TYR* 3.9 24.0 - - + +
168A MET* 4.4 2.5 - - - -
305A SER 5.0 0.7 - - - +
306A VAL* 3.7 25.4 - - + +
1328A SAH 4.9 0.7 + - - -
427D C 2.7 43.9 + - - +
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Residues in contact with ASN 120 (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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79A PHE* 3.0 49.7 + - + -
80A PRO 3.2 12.5 + - - -
81A CYS* 3.2 21.1 - - - +
84A PHE* 4.1 1.4 - - - -
119A GLU* 1.3 77.4 - - - +
121A VAL* 1.3 77.0 + - - +
124A PHE* 3.6 30.0 - - + -
165A ARG* 3.4 12.9 - - - +
166A ILE* 2.9 34.6 + - + -
168A MET* 4.4 0.9 - - + -
427D C 4.1 2.7 - - - +
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Residues in contact with VAL 121 (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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81A CYS* 3.6 18.4 - - + -
84A PHE 4.0 6.1 - - - +
85A SER* 3.6 31.9 - - - +
120A ASN* 1.3 92.5 + - - +
122A LYS* 1.3 67.8 + - - +
123A ASN 4.3 2.2 - - - +
124A PHE* 2.9 24.9 + - - +
165A ARG* 3.6 21.1 - - - +
166A ILE* 3.6 3.2 - - - +
427D C 3.4 42.6 - - + +
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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