Contacts of the strand formed by residues 59 - 66 (chain A) in PDB entry 3LEZ
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 ARG 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.5 3.6 - - - -
58A VAL* 1.3 72.4 - - - +
60A LEU* 1.3 60.4 + - - +
76A ARG* 4.1 14.1 - - - +
79A GLU* 3.3 34.5 + - - +
80A ARG 2.9 29.7 + - - +
81A PHE* 3.4 28.0 - - + +
187A PRO* 6.0 6.3 - - - +
277A SER* 3.2 8.0 - - - -
278A SER* 2.8 57.6 + - - +
279A ARG* 5.0 0.2 - - - +
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Residues in contact with LEU 60 (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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49A LEU* 3.7 29.4 - - + +
52A LEU* 4.1 24.2 - - + -
53A GLU* 2.9 20.6 + - + -
58A VAL* 4.3 5.6 - - + -
59A ARG* 1.3 73.8 - - - +
61A GLY* 1.3 59.3 + - - +
62A VAL* 3.8 19.5 - - + -
75A TYR* 3.3 14.2 - - + -
76A ARG* 3.3 20.4 - - - +
81A PHE* 3.8 3.8 - - - -
275A ILE* 3.8 22.4 - - + -
276A MET 3.6 14.8 - - - +
277A SER* 4.3 8.3 - - - -
290A LEU* 4.3 14.1 - - + -
294A ALA* 4.7 2.0 - - + -
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Residues in contact with GLY 61 (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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60A LEU* 1.3 72.8 - - - +
62A VAL* 1.3 66.6 + - - +
75A TYR 3.3 7.2 - - - -
76A ARG 3.9 6.5 - - - -
81A PHE* 3.5 19.4 - - - -
196A ALA* 3.8 9.3 - - - +
274A ALA 3.8 0.5 - - - +
275A ILE* 3.4 0.9 - - - -
276A MET 2.8 40.8 + - - +
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Residues in contact with VAL 62 (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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49A LEU* 3.9 28.5 - - + -
60A LEU* 3.8 26.9 - - + -
61A GLY* 1.3 79.8 - - - +
63A TYR* 1.3 70.3 + - - +
64A ALA* 5.1 0.4 - - + -
73A ILE* 4.7 4.9 - - + +
74A SER* 3.3 5.7 - - - -
75A TYR* 2.9 34.4 + - + +
77A GLU* 3.6 2.9 - - - +
196A ALA* 3.9 3.7 - - - +
273A ILE* 5.4 0.2 - - + -
274A ALA 3.4 7.6 - - - +
275A ILE* 4.4 14.6 - - + -
294A ALA* 4.6 2.2 - - + -
298A VAL* 3.8 28.9 - - + -
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Residues in contact with TYR 63 (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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62A VAL* 1.3 75.5 - - - +
64A ALA* 1.3 63.1 - - - +
65A ILE* 4.2 31.1 - - + +
72A GLU* 3.9 34.3 - - + +
73A ILE 3.6 2.0 - - - -
74A SER* 3.7 18.6 - - - -
77A GLU* 3.9 4.0 - - + -
196A ALA* 3.7 4.7 - - - +
197A LYS* 3.7 68.4 + - + +
200A ALA* 3.8 18.6 - - + +
201A THR* 4.6 7.6 - - - -
204A GLN* 6.1 0.2 - - - -
272A VAL 3.9 0.2 - - - +
273A ILE* 3.4 2.4 - - - +
274A ALA 2.8 34.2 + - - +
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Residues in contact with ALA 64 (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 TYR* 1.3 79.9 - - - +
65A ILE* 1.3 62.9 + - - +
66A ASP 4.3 0.2 - - - -
72A GLU* 3.0 5.5 - - - +
73A ILE* 2.9 40.7 + - + +
271A ILE* 4.4 1.3 - - + -
272A VAL 3.0 11.0 - - - +
273A ILE* 4.1 11.7 - - + -
298A VAL* 3.5 33.7 - - + -
302A LEU* 4.2 6.0 - - + +
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Residues in contact with ILE 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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63A TYR* 4.2 27.8 - - + +
64A ALA* 1.3 75.0 - - - +
66A ASP* 1.3 70.1 + - - +
67A THR* 3.6 7.5 + - + +
70A ASP* 5.6 1.8 - - - -
71A LYS 3.5 13.0 - - - +
72A GLU* 3.8 11.7 - - + -
200A ALA* 6.0 0.2 - - + -
204A GLN* 4.5 19.5 - - - +
270A PRO 4.1 0.2 - - - +
271A ILE* 3.3 4.1 - - - -
272A VAL* 2.9 52.6 + - + +
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Residues in contact with ASP 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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64A ALA 4.3 0.2 - - - -
65A ILE* 1.3 72.3 - - - +
67A THR* 1.3 59.0 + - - +
68A GLY* 2.9 16.8 + - - -
69A ALA* 2.9 24.3 + - + +
70A ASP* 2.9 31.0 + - - -
71A LYS 2.8 15.9 + - - +
269A GLU 4.4 2.3 - - - +
270A PRO 4.2 2.4 - - - +
271A ILE* 3.8 24.3 - - + +
302A LEU* 4.1 20.2 - - + +
303A ARG* 3.0 31.5 + - - -
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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