Contacts of the strand formed by residues 77 - 87 (chain A) in PDB entry 4PBZ
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A THR* 2.8 22.4 + - - +
71A HIS* 3.6 0.2 - - - -
72A THR* 3.0 42.8 + - - +
75A GLU 3.4 4.4 + - - -
76A GLN* 1.3 80.6 + - - +
78A HIS* 1.3 65.4 + - - +
123A HIS* 2.8 32.3 + - + +
125A GLY* 3.0 44.5 - - - +
126A GLU* 3.2 9.8 + - - +
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Residues in contact with HIS 78 (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 GLU* 6.0 0.4 - - - -
42A TRP* 5.8 2.9 - + - -
69A GLY* 3.6 0.5 - - - -
70A THR* 2.7 47.3 + - + +
76A GLN* 3.4 38.6 + - + +
77A ASN* 1.3 74.6 - - - +
79A LEU* 1.3 62.1 + - - +
80A VAL* 4.4 0.9 - - + -
120A LYS* 4.0 33.3 + - + +
121A ILE 3.1 21.3 - - - +
122A ASN* 3.6 22.7 + - - -
123A HIS* 3.8 6.5 - - - -
127A VAL* 3.3 6.8 - - - +
161A PRO* 4.2 18.3 - - + +
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Residues in contact with LEU 79 (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 VAL* 4.0 9.6 - - + -
68A LEU 3.4 19.1 - - - +
78A HIS* 1.3 71.7 - - - +
80A VAL* 1.3 62.2 + - - +
81A ILE* 5.7 1.5 - - + +
119A ILE* 4.0 1.0 - - - +
120A LYS* 3.6 3.3 - - - -
121A ILE* 2.9 50.7 + - + +
123A HIS* 4.0 13.6 - - + +
127A VAL* 4.3 5.6 - - + -
130A ALA* 3.7 26.0 - - + -
140A ILE* 3.8 29.2 - - + -
142A THR* 4.0 14.4 - - + -
152A PHE* 4.3 20.6 - - + -
154A TYR* 6.2 0.4 - - + -
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Residues in contact with VAL 80 (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 VAL* 3.4 7.1 - - - +
68A LEU* 2.9 54.1 + - + +
69A GLY* 4.4 6.3 - - - +
70A THR* 4.3 24.9 - - + -
78A HIS* 4.4 6.7 - - + +
79A LEU* 1.3 78.4 - - - +
81A ILE* 1.3 79.1 - - - +
82A ALA 4.2 0.2 - - - +
117A ILE* 4.0 26.2 - - + -
119A ILE 3.5 8.3 - - - +
120A LYS* 4.5 12.8 - - + -
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Residues in contact with ILE 81 (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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50A LEU* 4.1 14.4 - - + -
65A ARG* 3.7 30.1 - - - +
66A LEU 3.4 2.5 - - - +
67A VAL* 3.9 15.3 - - + -
79A LEU* 5.7 2.2 - - + -
80A VAL* 1.3 85.1 - - - +
82A ALA* 1.3 66.9 + - - +
117A ILE 3.9 0.5 - - - -
118A GLU* 2.9 27.6 + - + +
119A ILE* 3.1 42.0 + - + +
121A ILE* 6.3 0.9 - - + -
140A ILE* 3.8 28.7 - - + -
154A TYR* 4.4 11.7 - - + -
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Residues in contact with ALA 82 (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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40A LEU* 6.3 0.2 - - + -
65A ARG* 3.1 9.8 - - - +
66A LEU* 3.0 38.2 + - + +
68A LEU* 3.9 25.4 - - + -
80A VAL* 4.1 2.6 - - + -
81A ILE* 1.3 75.4 - - - +
83A SER* 1.3 64.1 + - - +
115A ILE* 4.6 10.3 - - + -
116A GLU 3.3 15.5 - - - +
117A ILE* 4.5 6.5 - - + -
118A GLU* 4.3 2.0 - - - +
399A MET* 5.8 0.2 - - + -
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Residues in contact with SER 83 (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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63A ILE* 3.9 19.9 - - - +
64A HIS 3.2 7.6 - - - -
65A ARG* 4.0 2.7 - - - -
82A ALA* 1.3 75.1 - - - +
84A VAL* 1.3 66.2 + - - +
85A GLN* 5.8 1.0 - - - +
114A LYS 5.3 1.2 + - - -
115A ILE* 3.4 7.6 - - - +
116A GLU* 2.8 43.2 + - - +
118A GLU* 3.6 31.5 + - - +
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Residues in contact with VAL 84 (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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36A MET* 4.2 16.8 - - + -
49A TRP* 4.1 17.7 - - + -
62A SER 3.6 0.5 - - - +
63A ILE* 3.5 4.2 - - - -
64A HIS* 2.5 38.5 + - - +
66A LEU* 3.7 30.1 - - + -
82A ALA* 5.1 1.1 - - + +
83A SER* 1.3 82.0 - - - +
85A GLN* 1.3 65.7 + - - +
86A LEU* 3.7 28.7 + - + -
114A LYS 3.8 4.0 - - - -
115A ILE* 4.0 15.5 - - + -
399A MET* 5.5 0.2 - - + -
401A VAL* 4.6 5.4 - - + -
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Residues in contact with GLN 85 (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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36A MET* 4.2 12.1 - - - +
61A PHE* 3.2 40.4 - - + -
62A SER 3.3 5.6 - - - +
63A ILE* 3.3 24.3 - - + +
83A SER* 5.8 1.6 - - - +
84A VAL* 1.3 75.0 - - - +
86A LEU* 1.3 64.6 + - - +
87A PRO* 4.2 3.0 - - - +
114A LYS* 3.2 47.2 + - - +
116A GLU* 5.4 6.1 + - - -
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Residues in contact with LEU 86 (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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34A LEU* 3.9 26.9 - - + -
36A MET* 4.2 4.5 - - - -
49A TRP* 4.7 2.2 - - + -
61A PHE* 3.2 4.7 - - - +
62A SER* 3.0 31.0 + - - +
64A HIS* 3.4 40.6 - - + +
84A VAL* 3.7 22.7 - - + -
85A GLN* 1.3 75.5 - - - +
87A PRO* 1.3 74.4 - - + +
383A ASN* 3.9 15.3 - - - +
386A GLU* 4.0 12.6 - - + -
389A VAL* 4.4 12.6 - - + -
401A VAL* 4.0 9.4 - - + -
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Residues in contact with PRO 87 (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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34A LEU* 4.1 29.2 - - + -
36A MET* 5.3 1.6 - - - -
60A ASP 3.8 8.3 - - - +
61A PHE* 4.4 2.0 - - + -
62A SER* 5.1 1.2 + - - -
85A GLN 4.2 4.7 - - - +
86A LEU* 1.3 92.9 - - + +
88A ASN* 1.3 63.0 + - - +
386A GLU* 5.1 9.5 - - - +
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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