Contacts of the strand formed by residues 120 - 128 (chain K) in PDB entry 3A2C
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 ILE 120 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105K VAL 4.4 5.6 - - - +
108K HIS* 3.3 54.7 - - + +
109K TRP* 3.9 42.6 - - + +
112K SER* 3.4 9.1 + - - +
118K VAL 3.7 0.4 + - - -
119K ARG* 1.3 83.2 + - - +
121K VAL* 1.3 64.9 + - - +
122K ASP 3.8 11.2 - - - +
123K VAL* 3.7 27.6 - - + -
136K ILE* 3.9 21.8 - - + -
137K VAL 4.0 2.5 - - - -
138K MET* 4.4 2.0 - - + +
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Residues in contact with VAL 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K TYR* 3.7 15.0 - - - +
90K PHE* 3.6 35.7 - - + -
109K TRP* 4.9 6.2 - - - -
119K ARG* 3.9 28.0 - - - +
120K ILE* 1.3 76.4 - - - +
122K ASP* 1.3 82.6 + - - +
137K VAL* 2.7 20.5 + - + +
138K MET 3.9 10.1 - - - -
139K GLU 4.0 3.4 - - - +
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Residues in contact with ASP 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K GLN* 6.3 0.2 - - - +
55K LYS* 3.9 18.7 + - + +
63K TYR* 3.0 21.2 + - - +
120K ILE* 3.8 3.7 - - - +
121K VAL* 1.3 111.2 - - - +
123K VAL* 1.3 68.4 + - - +
124K TYR* 3.5 33.0 + - + -
136K ILE 3.7 0.7 - - - -
137K VAL* 2.9 30.5 + - + +
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Residues in contact with VAL 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K LEU* 3.8 19.2 - - + +
53K GLN 4.9 4.2 + - - -
54K ILE* 3.2 23.8 - - + -
55K LYS* 2.8 26.3 + - - +
105K VAL* 3.7 33.7 - - + -
120K ILE* 3.7 19.7 - - + -
122K ASP* 1.3 79.4 - - - +
124K TYR* 1.3 71.0 + - - +
134K LEU* 4.5 10.3 - - + -
135K LEU 3.6 5.8 - - - +
136K ILE* 4.6 9.0 - - + -
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Residues in contact with TYR 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K ILE* 3.8 2.2 - - - -
55K LYS* 3.4 25.1 + - + +
57K ASN* 3.2 27.1 - - - -
59K ILE* 3.4 31.6 - - + -
62K ASP* 2.5 32.9 + - - +
63K TYR* 3.2 29.4 - + - -
122K ASP* 3.5 29.9 + - + -
123K VAL* 1.3 81.1 - - - +
125K GLU* 1.3 59.2 + - - +
126K ASN* 3.9 3.8 - - - +
134K LEU* 3.3 6.8 - - - +
135K LEU* 2.8 56.1 + - + +
137K VAL* 4.1 3.4 - - + -
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Residues in contact with GLU 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLY* 3.4 22.5 + - - -
52D LEU 4.7 1.6 + - - -
54K ILE* 3.4 16.3 - - + +
55K LYS 2.9 9.0 + - - +
56K LYS* 2.5 43.7 + - - +
97K ASP* 4.5 2.9 - - - +
102K ARG* 2.5 31.1 + - - +
124K TYR* 1.3 71.6 - - - +
126K ASN* 1.3 68.9 + - - +
132K LYS* 3.8 37.9 + - + +
133K CYS 3.5 7.0 - - - +
134K LEU* 4.2 9.4 - - + -
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Residues in contact with ASN 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D VAL* 3.7 16.7 - - + +
49D LYS 3.1 12.0 + - - +
51D GLY* 3.9 2.2 - - - +
56K LYS 3.6 7.7 + - - -
57K ASN 2.9 25.7 + - - -
58K ALA* 3.8 3.0 - - - +
59K ILE* 2.8 27.4 + - - +
124K TYR* 3.9 6.3 - - - +
125K GLU* 1.3 81.9 + - - +
127K LEU* 1.3 63.9 + - - +
128K TYR* 3.8 1.0 + - + -
132K LYS* 3.7 4.2 - - - +
133K CYS* 3.2 31.1 + - - +
135K LEU* 3.1 24.9 - - + +
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Residues in contact with LEU 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D VAL* 3.3 5.4 - - - +
49D LYS* 2.6 58.5 + - + +
50D SER 3.0 27.8 - - - +
51D GLY* 3.8 6.1 - - - -
52D LEU 4.8 0.2 - - - +
106D GLU* 6.1 0.4 - - - +
109D TRP* 3.6 22.9 - - + +
110D ARG* 3.8 23.3 - - + -
113D GLN* 4.6 6.3 - - - +
126K ASN* 1.3 72.1 - - - +
128K TYR* 1.3 59.3 + - - +
130K GLY 3.2 27.4 - - - +
131K ARG 3.2 9.6 - - - +
132K LYS* 3.9 16.8 - - + -
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Residues in contact with TYR 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D VAL* 4.2 31.9 - - + +
273E PRO* 4.4 9.9 - - + +
67K SER* 4.6 4.6 + - - -
70K LEU* 3.8 42.1 + - + +
71K GLY* 4.3 5.2 + - - -
74K ILE* 3.4 38.6 - - + -
94K MET* 6.1 0.7 - - - -
96K GLN* 5.3 1.0 + - - -
126K ASN 3.8 1.2 + - - -
127K LEU* 1.3 75.6 - - - +
129K ALA* 1.3 85.6 + - + +
130K GLY 3.0 0.4 - - - +
131K ARG* 2.8 25.7 + - - +
133K CYS* 3.8 16.5 - - - -
135K LEU* 6.3 0.7 - - + -
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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