Contacts of the strand formed by residues 118 - 124 (chain A) in PDB entry 1A9Z
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 ASN 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 4.9 1.8 - - - +
75A ASP* 2.9 27.5 + - - +
76A THR* 3.5 17.5 - - - +
77A VAL* 3.1 19.2 + - - +
111A MET* 3.7 7.7 - - - +
116A VAL* 3.8 1.3 - - - +
117A LYS* 1.3 85.1 + - - +
119A PHE* 1.3 61.4 + - - +
169A ASP 5.5 0.2 - - - +
171A SER* 3.3 15.4 - - - -
251A ALA* 4.1 11.8 - - - +
252A ASN* 3.0 51.3 + - - +
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Residues in contact with PHE 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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77A VAL* 3.5 13.0 - - + -
79A HIS* 3.4 40.6 - + + -
104A THR* 4.1 2.0 - - + -
107A LEU* 3.9 11.4 - - + -
108A ILE* 3.9 13.5 - - + -
111A MET* 3.4 30.7 - - + -
118A ASN* 1.3 74.1 - - - +
120A ILE* 1.3 67.3 - - - +
121A PHE* 3.7 22.2 - - + -
160A LEU* 3.8 31.0 - - + -
170A TRP* 4.0 17.3 - + + -
171A SER* 2.8 8.1 + - - +
172A ILE* 3.3 13.6 - - + -
173A ALA* 2.9 27.8 + - - +
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Residues in contact with ILE 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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76A THR* 4.8 5.4 - - - +
77A VAL 2.9 10.2 + - - +
78A ILE* 4.0 27.0 - - + +
79A HIS* 2.8 32.2 + - - +
119A PHE* 1.3 80.6 - - - +
121A PHE* 1.3 62.2 + - - +
173A ALA* 3.7 10.3 - - + -
175A LEU* 3.3 31.6 - - + -
243A HIS* 4.0 10.8 - - + +
246A ALA* 4.1 7.9 - - + +
247A MET* 3.4 46.4 - - + +
250A LEU* 6.2 1.1 - - + -
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Residues in contact with PHE 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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79A HIS* 3.8 31.0 - + - -
81A ALA 5.9 0.7 - - - -
104A THR* 4.3 3.6 - - - -
119A PHE* 3.7 16.5 - + + -
120A ILE* 1.3 76.6 - - - +
122A SER* 1.3 68.9 + - - +
123A SER* 3.0 25.0 + - - -
153A LYS* 3.5 48.2 - - + -
156A VAL* 3.5 34.3 - - + -
157A GLU* 4.4 3.4 - - + -
160A LEU* 3.9 17.0 - - + -
173A ALA 2.9 14.6 + - - +
174A LEU* 4.3 8.3 - - + -
175A LEU* 3.1 24.2 + - - +
177A TYR* 4.8 0.7 - - - -
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Residues in contact with SER 122 (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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78A ILE* 5.8 0.7 - - - +
79A HIS 3.3 16.6 + - - -
80A PHE* 3.1 19.1 - - - -
120A ILE 4.2 0.4 + - - -
121A PHE* 1.3 77.7 - - - +
123A SER* 1.3 60.3 + - - +
153A LYS* 2.7 26.5 + - - -
177A TYR* 2.6 29.3 + - - -
340A NAD 3.6 26.0 - - - -
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Residues in contact with SER 123 (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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121A PHE* 3.0 21.1 + - - -
122A SER* 1.3 76.6 - - - +
124A ALA* 1.3 69.2 + - - +
127A VAL* 3.7 9.2 - - - +
153A LYS* 4.4 6.0 - - - +
157A GLU* 2.6 35.4 + - - +
174A LEU 4.7 0.7 - - - -
175A LEU 2.7 29.1 + - - +
176A ARG* 4.0 1.9 - - - +
177A TYR* 3.4 10.6 + - - -
340A NAD 3.4 14.9 - - - -
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Residues in contact with ALA 124 (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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123A SER* 1.3 80.5 + - - +
125A ALA* 1.3 56.7 - - - +
126A THR* 2.9 20.5 + - + -
127A VAL* 3.1 29.4 + - - +
149A PHE* 4.8 2.0 - - + -
153A LYS* 4.6 9.6 - - + +
176A ARG* 3.9 6.8 - - - +
177A TYR 3.5 9.2 - - - +
340A NAD 3.8 13.9 - - + -
341A UPG 3.3 20.9 - - - +
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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