Contacts of the strand formed by residues 88 - 97 (chain A) in PDB entry 4HJU
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 HIS 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A THR* 4.1 8.7 + - - +
76A LYS* 3.5 20.4 - - - +
86A PRO* 3.7 5.5 - - - +
87A PHE* 1.3 100.3 - + - +
89A GLU* 1.3 64.7 + - - +
90A HIS 3.7 13.5 - - - +
112A SER 5.3 0.8 + - - -
113A PRO 4.5 3.2 + - - -
114A TYR 3.4 33.0 - - - -
115A SER* 3.8 9.7 + - - -
116A TYR* 3.8 27.6 - + + -
93B VAL* 3.7 29.4 - - + +
94B VAL 3.3 14.1 - - - +
107B ILE* 5.7 0.2 - - - +
118B THR* 4.2 8.0 + - + +
119B THR* 5.0 2.5 - - - -
120B ALA* 5.1 1.2 - - - +
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Residues in contact with GLU 89 (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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74A ASP* 4.8 1.6 - - - +
75A THR* 4.1 0.7 + - - -
76A LYS* 2.9 54.6 + - - +
87A PHE 3.9 0.9 + - - +
88A HIS* 1.3 75.3 - - - +
90A HIS* 1.3 75.7 + - + +
68B ILE* 4.1 24.3 - - + +
94B VAL* 2.8 36.9 + - + +
95B PHE* 4.1 4.7 - - - -
96B THR* 2.7 29.1 + - - +
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Residues in contact with HIS 90 (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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72A GLU* 3.0 29.2 + - + -
73A ILE 3.1 17.9 - - - +
74A ASP* 4.1 7.9 - - - +
75A THR* 3.3 11.2 - - - -
88A HIS* 3.4 15.2 - - - +
89A GLU* 1.3 88.2 + - + +
91A ALA* 1.3 60.8 + - - +
92A GLU* 3.1 39.7 + - - +
116A TYR* 4.3 4.5 + - - -
35B LYS* 6.0 1.4 + - - -
41B TRP* 5.7 4.2 - + - -
94B VAL* 3.8 32.5 + - + +
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Residues in contact with ALA 91 (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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71A VAL 3.6 2.1 - - - +
72A GLU* 3.6 0.3 - - - -
73A ILE* 2.8 45.6 + - + +
75A THR* 3.8 18.7 + - + -
90A HIS* 1.3 77.0 - - - +
92A GLU* 1.3 62.9 + - - +
93A VAL* 5.0 2.7 - - + -
109A ALA* 5.6 1.3 - - + -
111A LEU* 5.1 2.0 - - + -
116A TYR* 3.7 37.0 - - + -
118A THR* 6.4 0.7 - - - -
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Residues in contact with GLU 92 (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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70A LYS* 3.8 30.3 + - + +
71A VAL 3.4 4.7 - - - +
72A GLU* 3.1 27.3 - - + +
90A HIS* 3.1 29.9 + - + +
91A ALA* 1.3 73.0 - - - +
93A VAL* 1.3 61.2 + - - +
94A VAL* 4.1 1.9 + - + -
116A TYR* 4.4 5.9 + - - -
41B TRP* 5.7 4.5 + - - -
70B LYS* 4.5 3.3 - - - +
92B GLU* 3.3 48.8 + - + +
94B VAL* 4.2 8.7 - - + +
116B TYR* 3.0 20.4 + - - -
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Residues in contact with VAL 93 (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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69A TYR 3.7 1.4 - - - +
70A LYS* 3.4 1.2 - - - -
71A VAL* 2.8 43.7 + - + +
73A ILE* 4.8 11.0 - - + -
91A ALA* 4.9 3.4 - - + +
92A GLU* 1.3 81.5 - - - +
94A VAL* 1.3 61.8 + - - +
95A PHE* 3.9 16.6 - - + -
107A ILE* 4.0 31.9 - - + -
116A TYR* 6.1 0.4 - - + -
118A THR* 3.6 30.3 - - + +
119A THR 6.0 0.2 - - - +
87B PHE* 4.3 0.2 - - + -
88B HIS* 3.8 24.5 - - + +
116B TYR* 4.5 2.5 - - - -
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Residues in contact with VAL 94 (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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41A TRP* 3.9 12.1 - - + -
68A ILE* 3.8 19.3 - - + -
69A TYR 3.2 9.4 - - - +
70A LYS* 3.9 26.2 - - + -
92A GLU* 4.1 1.5 + - + -
93A VAL* 1.3 79.8 - - - +
95A PHE* 1.3 64.3 + - - +
88B HIS* 3.3 13.7 - - - +
89B GLU* 2.8 29.0 + - + -
90B HIS* 3.7 41.0 + - + +
92B GLU* 4.4 12.3 - - + +
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Residues in contact with PHE 95 (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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12A LEU* 4.3 12.6 - - + -
64A PHE* 4.7 2.7 - + - -
68A ILE* 4.3 2.5 - - - -
69A TYR* 2.8 50.2 + + + -
71A VAL* 3.8 27.8 - - + -
93A VAL* 3.9 10.3 - - + -
94A VAL* 1.3 82.2 - - - +
96A THR* 1.3 71.6 + - - +
97A ALA* 3.7 19.7 + - + -
105A TYR* 4.1 13.0 - + - -
107A ILE* 3.9 18.2 - - + -
87B PHE* 3.3 52.7 - + + +
89B GLU* 4.1 6.3 - - - -
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Residues in contact with THR 96 (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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67A GLY* 3.4 14.1 - - - +
68A ILE* 3.7 12.2 - - + +
95A PHE* 1.3 80.5 - - - +
97A ALA* 1.3 62.0 + - - +
99A ASP* 3.6 38.2 - - + +
105A TYR* 4.4 5.4 + - - -
76B LYS* 4.2 5.7 + - - -
87B PHE* 4.3 8.1 + - - +
89B GLU* 2.9 25.6 + - - -
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Residues in contact with ALA 97 (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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64A PHE* 3.8 13.2 - - + -
66A GLU* 3.3 17.7 - - - +
67A GLY 2.9 10.2 + - - +
69A TYR* 3.8 21.3 - - + -
95A PHE* 3.7 8.7 + - + -
96A THR* 1.3 75.7 - - - +
98A ASN* 1.3 83.3 + - - +
99A ASP* 3.2 4.9 + - - -
105A TYR* 3.4 13.9 - - + -
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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