Contacts of the strand formed by residues 38 - 43 (chain A) in PDB entry 5T78
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 LEU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A MET* 3.6 23.6 - - + -
23A CYS* 4.4 2.2 - - - -
29A ILE* 3.5 23.1 - - + -
36A ILE* 3.4 18.5 + - + -
37A TYR* 1.3 76.6 - - - +
39A GLU* 1.3 63.8 + - - +
40A TRP* 3.5 33.2 - - + +
53A ILE* 4.2 1.6 - - - +
54A TYR* 3.8 1.4 - - - -
55A ARG 3.4 5.5 + - - -
56A VAL* 3.0 31.7 + - + +
70A SER 5.6 0.2 - - - +
76A PHE* 3.6 40.6 - - + -
93A CYS* 4.7 2.2 - - + -
94A PHE 3.2 6.5 - - - +
95A GLN* 4.6 0.4 - - - +
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Residues in contact with GLU 39 (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 TYR* 4.3 9.4 - - - +
38A LEU* 1.3 81.4 - - - +
40A TRP* 1.3 64.3 + - - +
41A TYR* 2.5 44.8 + - + +
51A LEU* 4.2 0.4 - - + -
53A ILE 3.2 7.0 - - - +
54A TYR* 3.7 18.9 - - + +
55A ARG 4.4 1.5 + - - +
93A CYS* 3.3 7.1 - - - +
94A PHE* 2.7 45.7 + - + +
101B TYR 3.9 3.6 - - - +
102B GLY* 3.5 10.7 - - - -
5F ARG* 2.5 42.0 + - - +
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Residues in contact with TRP 40 (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 GLN* 4.2 4.7 - - - -
21A ILE* 3.8 35.7 - - + -
22A SER 4.5 0.2 - - - -
23A CYS* 3.7 22.0 - - + -
38A LEU* 3.5 20.5 - - + +
39A GLU* 1.3 76.6 - - - +
41A TYR* 1.3 61.2 + - - +
51A LEU* 3.6 5.0 - - - +
52A LEU* 2.9 29.6 + - + -
53A ILE* 2.8 42.2 + - + +
56A VAL 4.6 5.0 + - - -
69A GLY* 4.9 0.2 - - - -
70A SER 5.4 0.6 + - - +
77A THR 3.9 15.9 + - - +
78A LEU* 3.7 53.9 - - + +
91A TYR* 4.9 2.9 - - + -
92A TYR 3.4 20.9 - - - -
93A CYS* 3.5 23.8 - - + -
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Residues in contact with TYR 41 (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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39A GLU* 2.5 41.5 + - + -
40A TRP* 1.3 73.9 - - - +
42A LEU* 1.3 59.2 + - - +
49A PRO* 4.6 11.2 - - + -
50A LYS 3.2 10.3 - - - +
51A LEU* 3.5 31.7 - - + +
52A LEU* 4.5 3.1 - - - +
90A VAL 4.5 0.2 - - - -
91A TYR* 3.2 7.4 - - - +
92A TYR* 2.7 49.0 + - + +
94A PHE* 3.8 16.6 - + + -
103A PHE* 4.0 17.7 - + + -
45B LEU* 5.5 0.4 - - + -
103B PHE* 2.9 52.4 + + + +
106B TRP* 4.0 13.5 - + - -
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Residues in contact with LEU 42 (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 TYR* 1.3 73.0 - - - +
43A GLN* 1.3 71.2 + - - +
44A LYS* 3.7 37.8 + - + +
48A SER 4.2 0.9 - - - +
49A PRO* 3.5 1.7 - - - +
50A LYS* 2.9 35.4 + - + +
52A LEU* 3.8 28.2 - - + +
67A PHE* 5.2 4.3 - - + -
87A ASP* 4.1 7.2 - - - +
88A LEU 4.2 1.1 - - - +
89A GLY* 4.0 7.0 - - - -
90A VAL 3.5 19.1 - - - +
91A TYR* 3.7 39.5 - - + +
92A TYR* 5.5 0.2 - - - -
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Residues in contact with GLN 43 (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 TYR 4.3 0.2 - - - -
42A LEU* 1.3 72.8 - - - +
44A LYS* 1.3 65.5 + - - +
47A GLN 2.9 28.7 + - - +
48A SER 4.3 0.9 - - - -
49A PRO* 3.7 21.8 - - + +
89A GLY* 3.3 1.0 - - - -
90A VAL* 2.8 45.9 + - + +
92A TYR* 3.7 17.6 + - + -
39B GLN* 2.6 45.6 + - - -
43B LYS* 3.9 18.4 + - - +
95B TYR* 3.5 9.7 + - - -
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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