Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 4IHB
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 GLU 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL 4.5 0.9 - - - +
28A PHE* 3.4 10.1 - - - -
62A GLY 3.5 11.1 + - - +
63A SER* 1.3 81.6 - - - +
65A LEU* 1.3 64.4 + - - +
66A HIS* 3.9 2.8 + - + +
85A LYS* 3.9 37.5 - - + +
86A VAL 3.4 11.7 - - - +
87A PRO* 4.3 15.6 - - + +
88A LEU* 4.3 0.9 - - - -
89A ARG* 5.1 8.2 + - - +
201A FMT 3.2 22.3 + - - -
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Residues in contact with LEU 65 (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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2A LEU* 4.7 2.0 - - + -
4A VAL* 3.8 27.1 - - + -
26A ALA* 4.4 5.8 - - + -
27A VAL 3.9 7.9 - - - +
28A PHE* 3.8 26.5 - - + -
52A TRP* 4.0 21.3 - - + -
64A GLU* 1.3 71.5 - - - +
66A HIS* 1.3 60.4 + - - +
67A VAL* 3.8 11.5 + - + -
84A ALA 3.8 0.2 - - - +
85A LYS* 3.6 1.5 - - - -
86A VAL* 2.9 47.3 + - + +
88A LEU* 4.0 13.9 - - + +
119A LEU* 3.8 26.9 - - + -
121A VAL* 4.2 4.7 - - + -
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Residues in contact with HIS 66 (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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25A SER 3.6 1.0 - - - +
26A ALA* 3.3 4.0 - - - +
27A VAL* 3.0 51.2 + - + +
64A GLU 3.9 2.3 + - - +
65A LEU* 1.3 71.4 - - - +
67A VAL* 1.3 62.0 + - - +
68A VAL* 3.6 18.7 - - + +
83A GLU* 2.6 31.9 + - - -
84A ALA 3.4 17.5 - - - -
85A LYS* 3.5 36.2 + - + +
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Residues in contact with VAL 67 (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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6A ILE* 4.5 5.6 - - + -
24A CYS* 4.3 2.7 - - - -
25A SER 3.2 4.7 - - - +
26A ALA* 4.1 13.2 - - + -
65A LEU* 4.1 25.6 - - + +
66A HIS* 1.3 79.4 - - - +
68A VAL* 1.3 62.0 + - - +
83A GLU* 3.2 4.7 - - - +
84A ALA* 2.9 60.4 + - + +
86A VAL* 4.4 9.4 - - + -
105A LEU* 4.8 1.5 - - + +
117A LEU* 3.6 30.7 - - + -
119A LEU* 4.4 9.6 - - + -
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Residues in contact with VAL 68 (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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23A TYR* 3.9 0.3 - - - +
24A CYS* 3.3 1.9 - - - -
25A SER* 2.7 52.7 + - - +
66A HIS* 3.6 30.5 - - + +
67A VAL* 1.3 80.3 - - - +
69A VAL* 1.3 64.7 + - - +
70A LYS* 3.7 27.3 + - + +
80A PHE* 3.6 28.7 - - + -
82A GLY 3.5 5.6 - - - +
83A GLU* 3.9 7.2 - - + +
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Residues in contact with VAL 69 (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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9A ALA* 5.1 0.4 - - + -
12A VAL* 4.6 9.2 - - + -
22A ALA* 4.1 20.6 - - + -
23A TYR 3.5 11.0 - - - +
24A CYS* 4.5 14.1 - - - -
46A TRP* 4.3 16.2 - - + -
68A VAL* 1.3 74.9 - - - +
70A LYS* 1.3 64.7 + - - +
81A LEU* 2.8 33.1 + - + -
82A GLY 2.8 18.3 + - - +
105A LEU* 3.6 35.2 - - + -
117A LEU* 4.6 8.7 - - + -
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Residues in contact with LYS 70 (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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22A ALA* 3.2 3.6 - - - -
23A TYR* 3.0 70.2 + - + +
25A SER* 4.9 2.2 - - - -
32A LYS* 4.9 6.5 - - - +
34A ARG* 4.1 17.7 - - - +
68A VAL* 3.7 24.9 - - + +
69A VAL* 1.3 78.5 - - - +
71A ASP* 1.3 62.2 + - - +
78A ASN* 3.6 37.3 - - - +
79A ARG 3.3 13.2 - - - +
80A PHE* 3.9 7.2 - - - +
81A LEU* 3.6 6.7 - - - +
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Residues in contact with ASP 71 (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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14A THR* 2.3 36.7 + - + +
17A THR* 4.7 0.5 - - - +
19A ILE 4.3 1.9 - - - +
20A SER* 3.6 0.7 - - - -
21A ASP* 2.8 34.5 + - - +
70A LYS* 1.3 73.0 - - - +
72A HIS* 1.3 64.7 + - - +
73A GLU* 2.3 37.3 + - - +
74A THR 2.9 15.2 + - - +
78A ASN 3.7 2.1 - - - +
79A ARG* 2.9 38.7 + - + +
81A LEU* 3.4 15.0 - - + +
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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