Contacts of the strand formed by residues 141 - 147 (chain K) in PDB entry 5T0G
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 141 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76K CYS* 3.6 20.0 - - - -
77K ALA 3.4 5.4 - - - +
78K MET* 4.2 10.8 - - + -
85K ALA* 4.8 3.6 - - + -
88K LEU* 4.5 19.1 - - + -
89K ILE* 4.7 9.9 - - + -
116K VAL* 4.1 13.5 - - + -
139K VAL* 4.4 13.2 - - + +
140K ALA* 1.3 82.2 - - - +
142K LEU* 1.3 63.6 + - - +
143K PHE* 4.0 28.5 + - + -
155K HIS* 3.5 4.0 + - - -
156K MET* 2.9 59.6 + - + +
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Residues in contact with LEU 142 (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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37K ALA* 4.0 15.9 - - + +
39K GLY* 4.5 2.0 - - - +
48K LEU* 4.1 22.6 - - + +
76K CYS* 3.2 5.2 - - - -
77K ALA* 2.9 49.4 + - + +
79K SER* 5.1 0.4 - - - +
141K LEU* 1.3 71.0 - - - +
143K PHE* 1.3 64.2 + - - +
144K GLY 3.6 1.0 + - - -
153K LEU* 4.7 5.2 - - + -
154K PHE 3.4 4.9 - - - +
155K HIS* 3.4 35.0 - - + +
168K ARG* 4.3 20.4 - - + +
170K ILE* 3.9 36.8 - - + -
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Residues in contact with PHE 143 (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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70K ILE* 5.7 2.2 - - + -
74K ILE* 5.6 1.3 - - + -
75K GLY 4.1 4.3 - - - +
76K CYS* 3.5 32.5 - - + -
109K VAL* 4.5 7.6 - - + +
112K VAL* 3.8 35.4 - - + -
113K THR* 3.9 26.0 - - - -
116K VAL* 3.6 25.1 - - + -
141K LEU* 4.0 20.4 - - + -
142K LEU* 1.3 71.2 - - - +
144K GLY* 1.3 60.3 + - - +
152K GLN 3.9 0.7 - - - +
153K LEU* 3.2 5.3 - - - +
154K PHE* 2.6 58.4 + - + +
155K HIS 6.0 0.2 - - - -
156K MET* 4.2 19.1 - - + -
162K PHE* 5.9 0.4 - + - -
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Residues in contact with GLY 144 (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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46K VAL* 4.4 8.3 - - - -
48K LEU* 5.6 2.4 - - - +
74K ILE* 3.1 9.9 - - - +
75K GLY* 2.9 35.0 + - - +
76K CYS 4.4 0.2 - - - +
109K VAL* 4.2 2.9 - - - +
142K LEU 3.6 4.4 + - - -
143K PHE* 1.3 74.5 - - - +
145K GLY* 1.3 57.0 + - - -
152K GLN 3.6 8.3 - - - -
153K LEU* 4.0 10.0 - - - +
220K VAL* 5.4 1.6 - - - -
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Residues in contact with GLY 145 (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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46K VAL* 4.0 2.2 - - - +
73K HIS 3.3 16.6 - - - -
74K ILE* 3.8 3.8 - - - -
75K GLY 4.3 0.7 - - - -
109K VAL* 3.5 13.4 - - - +
144K GLY* 1.3 74.1 - - - -
146K VAL* 1.3 60.1 + - - +
152K GLN* 2.8 37.3 + - - +
220K VAL* 4.5 10.5 - - - +
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Residues in contact with VAL 146 (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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73K HIS* 3.0 33.9 + - + +
109K VAL* 3.5 3.8 - - - +
145K GLY* 1.3 76.4 - - - +
147K ASP* 1.3 66.5 + - - +
150K GLY* 3.4 20.4 - - - +
151K PRO* 3.8 16.6 - - + -
220K VAL* 4.2 21.5 - - + -
221K GLN* 4.5 3.6 - - - -
222K PRO* 3.7 37.7 - - + -
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Residues in contact with ASP 147 (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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73K HIS* 5.0 3.8 - - - -
108K THR* 4.4 3.7 - - - +
109K VAL* 3.4 30.0 - - + +
110K GLU* 5.3 5.5 + - - +
146K VAL* 1.3 82.3 - - - +
148K GLU* 1.3 74.2 - - - +
149K LYS* 3.2 36.2 + - - +
150K GLY 2.7 26.0 + - - +
152K GLN* 3.1 18.8 - - - +
154K PHE* 5.3 2.4 - - - -
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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