Contacts of the strand formed by residues 71 - 79 (chain s) in PDB entry 4PJO
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 ARG 71 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30s ARG* 5.0 0.4 - - - +
32s GLN* 4.5 3.2 - - - +
44s GLU* 3.2 41.0 + - - -
62s GLU* 2.9 35.6 + - - +
63s GLU 3.5 4.3 - - - +
64s ILE* 3.6 36.6 - - + +
69s LYS 5.1 3.1 - - - +
70s SER* 1.3 80.6 - - - +
72s LYS* 1.3 64.8 + - - +
73s GLN* 3.5 18.2 + - - +
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Residues in contact with LYS 72 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62s GLU* 3.1 5.6 - - - -
63s GLU* 2.9 50.0 + - + +
65s HIS* 4.2 20.2 - - + +
70s SER* 4.2 6.0 + - - -
71s ARG* 1.3 79.1 + - - +
73s GLN* 1.3 64.2 + - - +
74s LEU* 3.8 6.5 - - + +
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Residues in contact with GLN 73 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61s ALA 4.0 3.0 - - - +
62s GLU* 3.1 37.0 + - - +
71s ARG* 3.5 19.8 + - - +
72s LYS* 1.3 76.3 - - - +
74s LEU* 1.3 64.6 + - - +
75s GLY 5.2 0.9 - - - +
73t ARG* 5.3 3.3 + - - -
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Residues in contact with LEU 74 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43s ILE* 4.9 2.7 - - + -
61s ALA* 2.9 17.1 + - + +
62s GLU* 3.6 31.6 - - - +
63s GLU* 3.7 18.2 - - + +
72s LYS* 3.8 10.1 - - + +
73s GLN* 1.3 81.3 - - - +
75s GLY* 1.3 63.0 + - - +
76s ARG 4.0 0.7 + - - -
77s ILE* 3.7 27.4 - - + -
71t TYR* 3.4 30.1 - - + +
73t ARG* 3.6 38.8 + - - +
74t GLY 5.2 1.4 - - - +
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Residues in contact with GLY 75 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58s LEU 3.7 0.2 - - - +
59s ASP 3.3 9.1 - - - +
60s ASP* 4.5 9.3 + - - -
61s ALA* 3.0 32.7 + - - +
73s GLN* 5.2 1.2 - - - +
74s LEU* 1.3 80.4 - - - +
76s ARG* 1.3 61.8 + - - -
77s ILE* 4.1 0.2 - - - -
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Residues in contact with ARG 76 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48s ILE* 3.1 23.9 - - + +
57s VAL* 4.2 4.7 - - + -
58s LEU 3.4 10.8 - - - +
59s ASP* 2.3 37.9 + - - +
74s LEU 4.0 0.6 + - - -
75s GLY* 1.3 70.8 - - - -
77s ILE* 1.3 63.9 + - - +
2t SER* 4.1 14.3 + - - -
5t LEU* 3.2 24.7 - - - +
10t PHE* 3.6 40.5 - - + -
73t ARG* 3.7 13.2 - - - +
74t GLY 3.9 4.3 + - - -
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Residues in contact with ILE 77 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43s ILE* 4.1 12.1 - - + -
56s LEU 3.6 0.2 - - - +
57s VAL* 3.3 4.9 - - - +
58s LEU* 2.8 54.6 + - + -
61s ALA* 3.6 21.8 - - + -
74s LEU* 3.7 30.3 - - + -
75s GLY 3.8 6.3 - - - +
76s ARG* 1.3 80.5 - - - +
78s MET* 1.3 64.4 + - - +
79s LEU* 4.6 3.8 - - + -
10t PHE* 4.0 5.4 - - - -
71t TYR* 4.2 24.7 - - + -
72t ILE 3.4 9.6 - - - +
73t ARG* 3.7 16.6 - - + -
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Residues in contact with MET 78 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55s ASN* 3.9 23.8 - - - -
56s LEU 3.2 12.8 - - - +
57s VAL* 4.5 1.6 - - + +
77s ILE* 1.3 73.4 - - - +
79s LEU* 1.3 64.3 + - - +
80s LYS* 4.1 8.5 + - + +
7t PRO* 4.0 19.3 - - + -
10t PHE* 3.6 22.7 - - + -
11t LEU* 3.3 42.0 - - + -
40t MET* 3.5 21.1 - - + +
42t MET* 5.2 2.2 - - + -
71t TYR* 3.1 5.9 - - - +
72t ILE* 2.9 42.0 + - + +
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Residues in contact with LEU 79 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33s VAL* 4.2 17.5 - - + -
35s LEU* 4.3 8.3 - - + -
43s ILE* 3.7 26.5 - - + -
54s MET 4.5 0.5 - - - +
55s ASN* 3.4 3.5 - - - +
56s LEU* 2.9 42.6 + - + +
58s LEU* 4.5 13.5 - - + -
77s ILE* 4.0 2.6 - - + -
78s MET* 1.3 75.0 - - - +
80s LYS* 1.3 69.0 + - - +
83s ASN* 5.1 0.2 - - + -
84s ILE* 3.8 31.9 - - + -
70t LEU* 3.7 31.9 - - + +
71t TYR* 4.0 6.3 - - + -
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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