Contacts of the strand formed by residues 85 - 95 (chain A) in PDB entry 2DT4
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS* 4.4 13.5 - - - +
31A LYS* 3.4 28.6 - - - +
81A LEU* 3.4 6.2 - - - +
82A LYS 2.9 31.4 + - - +
83A ASP 4.2 7.4 - - - +
84A GLY* 1.3 86.5 - - - +
86A PRO* 1.3 82.6 - - + +
87A PHE* 4.1 0.7 - - - +
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Residues in contact with PRO 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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27A LYS* 3.6 29.7 + - + +
30A CYS* 4.0 5.4 - - + -
31A LYS* 3.7 32.3 - - + +
35A ILE 3.6 24.7 - - - +
36A GLU* 4.7 7.2 - - + +
79A VAL* 3.8 16.2 - - + -
80A SER 3.8 6.7 - - - +
81A LEU* 4.6 1.8 - - + -
84A GLY 4.8 0.4 - - - +
85A GLU* 1.3 97.1 - - + +
87A PHE* 1.3 57.1 + - - +
88A VAL* 5.3 0.7 - - - -
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Residues in contact with PHE 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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27A LYS* 5.5 7.9 - - + -
78A ASN 3.7 1.0 - - - +
79A VAL* 3.3 4.7 - - - +
80A SER* 2.9 36.2 + - - +
82A LYS* 3.6 50.3 - - + +
85A GLU 4.1 0.9 - - - +
86A PRO* 1.3 74.3 - - - +
88A VAL* 1.3 82.0 + - - +
89A HIS* 3.9 9.8 + + + -
128A ARG* 3.7 31.0 + - - -
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Residues in contact with VAL 88 (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 LEU* 3.7 42.0 - - + +
26A ILE* 3.9 18.6 - - + -
27A LYS* 3.6 38.1 - - + +
40A ILE* 3.8 27.1 - - + -
78A ASN 3.6 4.3 - - - +
79A VAL* 4.3 8.5 - - + -
87A PHE* 1.3 92.3 - - - +
89A HIS* 1.3 62.7 + - - +
90A ALA 4.2 0.6 + - - -
105A HIS* 5.7 1.0 + - - -
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Residues in contact with HIS 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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61A TYR* 3.8 13.7 - + - -
77A GLY* 3.2 2.4 - - - -
78A ASN* 2.9 40.6 + - - +
87A PHE* 3.9 8.2 + + + -
88A VAL* 1.3 73.4 + - - +
90A ALA* 1.3 61.1 + - - +
91A HIS* 3.9 13.5 + + - -
105A HIS* 3.3 37.4 + + - -
128A ARG* 3.5 43.5 - - - +
137A LEU* 6.5 0.2 - - + -
1144A GOL 3.0 26.6 + - - -
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Residues in contact with ALA 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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23A LEU* 4.4 16.6 - - + +
40A ILE* 4.4 6.7 - - + -
75A LEU* 4.1 30.3 - - + -
76A ILE 3.4 12.8 - - - +
77A GLY* 4.0 2.2 - - - -
88A VAL 4.2 0.8 - - - -
89A HIS* 1.3 77.8 + - - +
91A HIS* 1.3 66.8 + - - +
105A HIS* 3.4 10.2 + - - -
106A LEU* 2.8 25.8 + - + +
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Residues in contact with HIS 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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74A SER* 3.8 1.0 + - - +
75A LEU* 3.5 1.0 - - - +
76A ILE* 3.0 33.0 + - + +
89A HIS* 3.9 12.9 + + - -
90A ALA* 1.3 82.0 - - - +
92A VAL* 1.3 67.5 + - - +
104A GLY* 3.3 11.6 - - - +
105A HIS* 3.7 21.8 + - - +
106A LEU 4.1 0.2 - - - +
1144A GOL 3.4 40.2 + - - -
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Residues in contact with VAL 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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46A LEU* 4.9 1.1 - - + -
51A ILE* 3.8 26.9 - - + -
72A LEU* 3.5 26.0 - - + -
74A SER* 3.2 7.2 - - - +
75A LEU* 3.9 19.1 - - + -
91A HIS* 1.3 81.8 - - - +
93A SER* 1.3 60.0 - - - +
94A LEU* 4.0 12.6 - - + -
103A GLY* 3.2 4.5 - - - -
104A GLY 2.9 33.5 + - - +
106A LEU* 3.9 30.5 - - + -
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Residues in contact with SER 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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71A GLU 3.7 0.3 - - - +
72A LEU* 3.8 0.5 - - - -
73A ILE* 2.9 38.9 + - - +
74A SER* 2.7 35.9 + - - +
92A VAL* 1.3 73.5 - - - +
94A LEU* 1.3 66.4 + - - +
101A VAL* 3.8 19.5 - - - -
102A PHE 3.4 4.3 - - - -
103A GLY* 4.4 0.7 - - - -
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Residues in contact with LEU 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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46A LEU* 4.2 14.8 - - + -
49A PRO* 3.7 14.8 - - + -
51A ILE* 3.7 23.6 - - + -
66A LEU* 3.7 25.6 - - + -
70A TYR* 3.9 24.2 - - + -
71A GLU 3.1 11.4 - - - +
72A LEU* 4.0 20.0 - - + -
73A ILE* 4.0 3.6 - - - -
92A VAL* 4.0 11.4 - - + -
93A SER* 1.3 81.8 - - - +
95A GLY* 1.3 59.9 + - - +
100A ILE 3.6 1.2 - - - +
101A VAL* 3.2 3.3 - - - +
102A PHE* 2.7 42.7 + - + +
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Residues in contact with GLY 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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69A SER 4.5 0.3 - - - +
70A TYR* 3.3 8.5 - - - -
71A GLU* 2.8 46.1 + - - +
73A ILE* 3.5 18.1 - - - +
94A LEU* 1.3 73.0 - - - +
96A ASN* 1.3 66.0 + - - -
99A GLY* 5.2 3.1 - - - -
100A ILE 3.5 6.3 - - - -
101A VAL* 4.6 0.4 - - - -
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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