Contacts of the strand formed by residues 90 - 97 (chain A) in PDB entry 4DKT
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 GLN 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A SER* 2.6 31.7 + - - +
46A PRO* 4.8 2.1 - - - +
47A GLY* 3.3 29.5 + - - +
48A VAL* 3.6 8.3 + - + -
80A MET* 3.3 33.7 - - + -
82A ALA 5.6 2.3 + - - +
84A SER* 4.4 2.6 - - - +
88A GLY 3.1 5.3 - - - +
89A ASP* 1.3 100.6 + - - +
91A LYS* 1.3 63.0 + - - +
109A TYR* 3.7 0.3 - - - -
110A LEU* 2.8 31.6 + - + +
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Residues in contact with LYS 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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43A ASN 4.4 0.2 - - - +
44A ALA* 3.4 3.6 - - - +
45A SER* 2.9 43.6 + - - +
48A VAL* 4.6 0.9 - - - +
88A GLY 5.4 1.3 - - - +
89A ASP 5.5 1.3 - - - +
90A GLN* 1.3 77.0 - - - +
92A VAL* 1.3 68.9 + - - +
93A GLN* 5.4 11.7 + - - -
107A LEU* 4.8 13.9 - - - +
108A LEU 3.2 13.2 - - - +
109A TYR* 3.8 32.3 + - + -
110A LEU 4.5 0.4 - - - +
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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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27A LEU* 4.9 6.1 - - + -
42A ILE* 4.2 18.6 - - + -
43A ASN 3.7 8.7 - - - +
44A ALA* 4.0 7.4 - - + -
48A VAL* 4.0 14.4 - - + -
50A VAL* 5.9 0.2 - - + -
78A LEU* 3.9 18.8 - - + -
91A LYS* 1.3 81.2 - - - +
93A GLN* 1.3 66.1 + - - +
94A ILE* 4.4 13.5 - - + -
106A ALA 4.6 0.2 - - - -
107A LEU* 3.8 1.9 - - - +
108A LEU* 2.9 44.6 + - + +
110A LEU* 3.4 28.7 - - + -
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Residues in contact with GLN 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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41A SER 3.8 0.7 - - - +
42A ILE* 3.6 3.1 - - - -
43A ASN* 2.9 62.1 + - + +
91A LYS* 5.4 11.7 + - - -
92A VAL* 1.3 76.5 - - - +
94A ILE* 1.3 66.2 + - - +
95A SER* 4.1 13.0 + - - +
105A LYS* 3.9 35.3 + - + +
106A ALA 3.4 9.0 - - - +
107A LEU* 4.8 10.2 - - + +
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Residues in contact with ILE 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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9A VAL* 4.0 28.3 - - + -
27A LEU* 4.3 14.6 - - + -
29A ILE* 4.2 15.3 - - + -
40A PHE* 4.4 4.7 - - + -
41A SER 3.5 8.3 - - - +
42A ILE* 4.0 26.7 - - + -
92A VAL* 4.4 10.5 - - + +
93A GLN* 1.3 77.3 - - - +
95A SER* 1.3 64.5 + - - +
96A TYR* 3.8 30.7 + - + +
104A VAL 3.6 2.1 - - - +
105A LYS* 3.2 4.3 - - - -
106A ALA* 2.8 50.9 + - + +
108A LEU* 4.9 2.7 - - + -
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Residues in contact with SER 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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40A PHE* 3.1 6.5 - - - -
41A SER* 2.9 48.4 + - - -
43A ASN* 6.0 0.5 - - - +
93A GLN* 4.1 19.6 + - - +
94A ILE* 1.3 73.8 - - - +
96A TYR* 1.3 62.1 + - - +
97A TYR* 3.8 6.8 + - - -
103A PRO* 4.6 16.3 - - - +
104A VAL 3.8 3.8 - - - -
105A LYS* 4.4 5.3 - - - +
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Residues in contact with TYR 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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9A VAL* 3.9 24.8 + - - +
11A PRO* 3.6 24.3 - - + +
29A ILE* 3.2 44.8 + - + +
33A ALA* 3.9 7.8 - - + -
34A PRO* 3.5 23.8 - - + -
37A CYS* 3.3 26.7 - - + -
39A SER 3.6 2.9 - - - -
40A PHE* 4.1 12.1 - - + -
70A LEU* 4.3 10.8 - - + -
94A ILE* 3.8 16.0 - - + +
95A SER* 1.3 70.3 - - - +
97A TYR* 1.3 59.4 + - - +
102A PRO 4.2 0.5 - - - +
103A PRO* 3.4 1.8 - - - +
104A VAL 2.9 51.6 + - - +
106A ALA* 3.9 15.6 - - + +
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Residues in contact with TYR 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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37A CYS* 3.7 7.7 - - - -
38A THR* 3.2 3.8 + - - -
39A SER* 2.8 54.9 + - - +
40A PHE 3.8 20.5 + - - -
41A SER* 4.0 12.1 - - - -
67A THR* 3.0 36.9 + - - +
95A SER* 3.8 14.8 - - - -
96A TYR* 1.3 75.1 - - - +
98A GLY* 1.3 66.0 + - - +
101A THR* 4.5 4.5 - - - +
103A PRO* 4.1 25.8 - - + -
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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